From 801ae0fd10c2ab14ccd8f2bc3ccd7d6327935068 Mon Sep 17 00:00:00 2001 From: rlegendr <rachel.legendre@pasteur.fr> Date: Fri, 4 Oct 2024 14:52:59 +0200 Subject: [PATCH] delete logs --- ...omplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.err | 30 ---- ...omplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.out | 0 ...omplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.err | 30 ---- ...omplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.out | 0 ...omplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.err | 30 ---- ...omplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.out | 0 ...mplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.err | 30 ---- ...mplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.out | 0 ...mplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.err | 30 ---- ...mplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.out | 0 ...mplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.err | 30 ---- ...mplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.out | 0 ...omplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.err | 30 ---- ...omplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.out | 0 ...omplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.err | 30 ---- ...omplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.out | 0 ...omplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.err | 30 ---- ...omplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.out | 0 ...mCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.err | 36 ---- ...mCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.out | 0 ...mCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.err | 36 ---- ...mCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.out | 0 ...mCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.err | 36 ---- ...mCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.out | 0 ...Coverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.err | 36 ---- ...Coverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.out | 0 ...Coverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.err | 36 ---- ...Coverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.out | 0 ...Coverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.err | 36 ---- ...Coverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.out | 0 ...mCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.err | 36 ---- ...mCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.out | 0 ...mCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.err | 36 ---- ...mCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.out | 0 ...mCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.err | 36 ---- ...mCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.out | 0 ...ge_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err | 39 ----- ...ge_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out | 1 - ...ge_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err | 39 ----- ...ge_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out | 0 ...ge_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err | 39 ----- ...ge_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out | 1 - ...ge_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err | 39 ----- ...ge_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out | 0 ...ge_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err | 39 ----- ...ge_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out | 1 - ...ge_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err | 39 ----- ...ge_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out | 0 ...ge_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err | 39 ----- ...ge_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out | 1 - ...ge_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err | 39 ----- ...ge_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out | 0 ...rage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err | 39 ----- ...rage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out | 1 - ...rage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err | 39 ----- ...rage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out | 0 ...rage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err | 39 ----- ...rage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out | 1 - ...rage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err | 39 ----- ...rage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out | 0 ...rage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err | 39 ----- ...rage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out | 1 - ...rage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err | 39 ----- ...rage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out | 0 ...rage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err | 39 ----- ...rage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out | 1 - ...rage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err | 39 ----- ...rage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out | 0 ...erage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err | 39 ----- ...erage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out | 1 - ...erage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err | 39 ----- ...erage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out | 0 ...erage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err | 39 ----- ...erage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out | 1 - ...erage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err | 39 ----- ...erage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out | 0 ...erage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err | 39 ----- ...erage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out | 1 - ...erage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err | 39 ----- ...erage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out | 0 ...erage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err | 39 ----- ...erage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out | 1 - ...erage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err | 39 ----- ...erage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out | 0 .../bam_to_bigwig_SAMPLE=ATAC_D0_rep1.err | 30 ---- .../bam_to_bigwig_SAMPLE=ATAC_D0_rep1.out | 0 .../bam_to_bigwig_SAMPLE=ATAC_D0_rep2.err | 30 ---- .../bam_to_bigwig_SAMPLE=ATAC_D0_rep2.out | 0 .../bam_to_bigwig_SAMPLE=ATAC_D0_rep3.err | 30 ---- .../bam_to_bigwig_SAMPLE=ATAC_D0_rep3.out | 0 .../bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.err | 30 ---- .../bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.out | 0 .../bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.err | 30 ---- .../bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.out | 0 .../bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.err | 30 ---- .../bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.out | 0 .../bam_to_bigwig_SAMPLE=ATAC_D6_rep1.err | 30 ---- .../bam_to_bigwig_SAMPLE=ATAC_D6_rep1.out | 0 .../bam_to_bigwig_SAMPLE=ATAC_D6_rep2.err | 30 ---- .../bam_to_bigwig_SAMPLE=ATAC_D6_rep2.out | 0 .../bam_to_bigwig_SAMPLE=ATAC_D6_rep3.err | 30 ---- .../bam_to_bigwig_SAMPLE=ATAC_D6_rep3.out | 0 ...ff_CALLER=genrich.MOD=narrow.MARK=ATAC.err | 31 ---- ...ff_CALLER=genrich.MOD=narrow.MARK=ATAC.out | 0 ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err | 31 ---- ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out | 0 ...o_gff_CALLER=macs2_narrow.MARK=H3K27ac.err | 33 ---- ...o_gff_CALLER=macs2_narrow.MARK=H3K27ac.out | 0 ...d_to_gff_CALLER=macs2_narrow.MARK=Klf4.err | 33 ---- ...d_to_gff_CALLER=macs2_narrow.MARK=Klf4.out | 0 ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.err | 31 ---- ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.out | 0 ...2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.err | 55 ------ ...2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.out | 0 ...2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.err | 55 ------ ...2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.out | 0 ...2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.err | 55 ------ ...2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.out | 0 ..._mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.err | 55 ------ ..._mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.out | 0 ..._mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.err | 55 ------ ..._mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.out | 0 ..._mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.err | 55 ------ ..._mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.out | 0 ...2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.err | 55 ------ ...2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.out | 0 ...2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.err | 55 ------ ...2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.out | 0 ...2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.err | 55 ------ ...2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.out | 0 ...ng_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err | 58 ------- ...ng_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out | 1 - ...ng_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err | 58 ------- ...ng_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out | 0 ...ng_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err | 58 ------- ...ng_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out | 1 - ...ng_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err | 58 ------- ...ng_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out | 0 ...ng_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err | 58 ------- ...ng_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out | 1 - ...ng_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err | 58 ------- ...ng_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out | 0 ...ng_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err | 58 ------- ...ng_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out | 1 - ...ng_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err | 58 ------- ...ng_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out | 0 ...ping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err | 58 ------- ...ping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out | 1 - ...ping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err | 58 ------- ...ping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out | 0 ...ping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err | 58 ------- ...ping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out | 1 - ...ping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err | 58 ------- ...ping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out | 0 ...ping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err | 58 ------- ...ping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out | 1 - ...ping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err | 58 ------- ...ping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out | 0 ...ping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err | 58 ------- ...ping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out | 1 - ...ping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err | 58 ------- ...ping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out | 0 ...pping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err | 58 ------- ...pping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out | 1 - ...pping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err | 58 ------- ...pping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out | 0 ...pping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err | 58 ------- ...pping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out | 1 - ...pping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err | 58 ------- ...pping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out | 0 ...pping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err | 58 ------- ...pping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out | 1 - ...pping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err | 58 ------- ...pping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out | 0 ...pping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err | 58 ------- ...pping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out | 1 - ...pping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err | 58 ------- ...pping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out | 0 ...wr_CALLER=genrich.MOD=narrow.MARK=ATAC.err | 45 ----- ...wr_CALLER=genrich.MOD=narrow.MARK=ATAC.out | 38 ----- ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err | 45 ----- ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out | 38 ----- ...flowr_CALLER=macs2_narrow.MARK=H3K27ac.err | 75 -------- ...flowr_CALLER=macs2_narrow.MARK=H3K27ac.out | 4 - ...hipflowr_CALLER=macs2_narrow.MARK=Klf4.err | 47 ----- ...hipflowr_CALLER=macs2_narrow.MARK=Klf4.out | 38 ----- ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.err | 45 ----- ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.out | 38 ----- ...ation_CALLER=macs2_narrow.MARK=H3K27ac.err | 63 ------- ...ation_CALLER=macs2_narrow.MARK=H3K27ac.out | 0 ...notation_CALLER=macs2_narrow.MARK=Klf4.err | 63 ------- ...notation_CALLER=macs2_narrow.MARK=Klf4.out | 0 ...it_CALLER=genrich.MOD=narrow.MARK=ATAC.err | 26 --- ...it_CALLER=genrich.MOD=narrow.MARK=ATAC.out | 0 ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err | 26 --- ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out | 0 ..._init_CALLER=macs2_narrow.MARK=H3K27ac.err | 28 --- ..._init_CALLER=macs2_narrow.MARK=H3K27ac.out | 0 ...owr_init_CALLER=macs2_narrow.MARK=Klf4.err | 28 --- ...owr_init_CALLER=macs2_narrow.MARK=Klf4.out | 0 ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.err | 26 --- ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.out | 0 ...MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err | 31 ---- ...MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.out | 0 ...MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err | 31 ---- ...MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.out | 0 ...OD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err | 31 ---- ...OD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.out | 0 ...MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err | 31 ---- ...MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.out | 0 ...MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err | 31 ---- ...MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.out | 0 ...OD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err | 31 ---- ...OD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.out | 0 ...=macs2_narrow.MARK=H3K27ac.COND=shCtrl.err | 35 ---- ...=macs2_narrow.MARK=H3K27ac.COND=shCtrl.out | 0 ...=macs2_narrow.MARK=H3K27ac.COND=shUbc9.err | 35 ---- ...=macs2_narrow.MARK=H3K27ac.COND=shUbc9.out | 0 ...LER=macs2_narrow.MARK=Klf4.COND=shCtrl.err | 35 ---- ...LER=macs2_narrow.MARK=Klf4.COND=shCtrl.out | 0 ...LER=macs2_narrow.MARK=Klf4.COND=shUbc9.err | 35 ---- ...LER=macs2_narrow.MARK=Klf4.COND=shUbc9.out | 0 ...OD=noModel.FORM=narrow.IP_NAME=ATAC_D0.err | 31 ---- ...OD=noModel.FORM=narrow.IP_NAME=ATAC_D0.out | 0 ...OD=noModel.FORM=narrow.IP_NAME=ATAC_D6.err | 31 ---- ...OD=noModel.FORM=narrow.IP_NAME=ATAC_D6.out | 0 ...D=noModel.FORM=narrow.IP_NAME=ATAC_D6F.err | 31 ---- ...D=noModel.FORM=narrow.IP_NAME=ATAC_D6F.out | 0 ...ix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err | 32 ---- ...ix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out | 0 ...ix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err | 32 ---- ...ix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out | 0 ...ix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err | 32 ---- ...ix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out | 0 ...ix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err | 32 ---- ...ix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out | 0 ...trix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err | 32 ---- ...trix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out | 0 ...trix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err | 32 ---- ...trix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out | 0 ...trix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err | 32 ---- ...trix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out | 0 ...trix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err | 32 ---- ...trix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out | 0 ...atrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err | 32 ---- ...atrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out | 0 ...atrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err | 32 ---- ...atrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out | 0 ...atrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err | 32 ---- ...atrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out | 0 ...atrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err | 32 ---- ...atrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out | 0 ...ute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.err | 52 ------ ...ute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.out | 0 ...ute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.err | 52 ------ ...ute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.out | 0 ...e_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..err | 52 ------ ...e_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..out | 0 ...e_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..err | 52 ------ ...e_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..out | 0 ...ute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.err | 52 ------ ...ute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.out | 0 ...ute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.err | 52 ------ ...ute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.out | 0 ...e_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..err | 52 ------ ...e_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..out | 0 ...e_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..err | 52 ------ ...e_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..out | 0 ...ompute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.err | 52 ------ ...ompute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.out | 0 ...ompute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.err | 52 ------ ...ompute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.out | 0 ...pute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..err | 52 ------ ...pute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..out | 0 ...pute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..err | 52 ------ ...pute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..out | 0 ...ompute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.err | 52 ------ ...ompute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.out | 0 ...ompute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.err | 52 ------ ...ompute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.out | 0 ...pute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..err | 52 ------ ...pute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..out | 0 ...pute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..err | 52 ------ ...pute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..out | 0 .../cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.err | 51 ------ .../cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.out | 0 .../cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.err | 51 ------ .../cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.out | 0 .../cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.err | 51 ------ .../cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.out | 0 .../cutadapt_SAMPLE=ATAC_D6F_rep1.err | 51 ------ .../cutadapt_SAMPLE=ATAC_D6F_rep1.out | 0 .../cutadapt_SAMPLE=ATAC_D6F_rep2.err | 51 ------ .../cutadapt_SAMPLE=ATAC_D6F_rep2.out | 0 .../cutadapt_SAMPLE=ATAC_D6F_rep3.err | 51 ------ .../cutadapt_SAMPLE=ATAC_D6F_rep3.out | 0 .../cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.err | 51 ------ .../cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.out | 0 .../cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.err | 51 ------ .../cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.out | 0 .../cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.err | 51 ------ .../cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.out | 0 .../cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.err | 54 ------ .../cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.out | 0 .../cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.err | 54 ------ .../cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.out | 0 .../cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.err | 54 ------ .../cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.out | 0 .../cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.err | 54 ------ .../cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.out | 0 .../cutadapt_SAMPLE=INPUT_shCtrl_Rep1.err | 54 ------ .../cutadapt_SAMPLE=INPUT_shCtrl_Rep1.out | 0 .../cutadapt_SAMPLE=INPUT_shCtrl_Rep2.err | 54 ------ .../cutadapt_SAMPLE=INPUT_shCtrl_Rep2.out | 0 .../cutadapt_SAMPLE=INPUT_shUbc9_Rep1.err | 54 ------ .../cutadapt_SAMPLE=INPUT_shUbc9_Rep1.out | 0 .../cutadapt_SAMPLE=INPUT_shUbc9_Rep2.err | 54 ------ .../cutadapt_SAMPLE=INPUT_shUbc9_Rep2.out | 0 .../cutadapt_SAMPLE=Klf4_shCtrl_Rep1.err | 54 ------ .../cutadapt_SAMPLE=Klf4_shCtrl_Rep1.out | 0 .../cutadapt_SAMPLE=Klf4_shCtrl_Rep2.err | 54 ------ .../cutadapt_SAMPLE=Klf4_shCtrl_Rep2.out | 0 .../cutadapt_SAMPLE=Klf4_shUbc9_Rep1.err | 54 ------ .../cutadapt_SAMPLE=Klf4_shUbc9_Rep1.out | 0 .../cutadapt_SAMPLE=Klf4_shUbc9_Rep2.err | 54 ------ .../cutadapt_SAMPLE=Klf4_shUbc9_Rep2.out | 0 .../fastqc/fastqc_SAMPLE=ATAC_D0_rep1.err | 71 -------- .../fastqc/fastqc_SAMPLE=ATAC_D0_rep1.out | 0 .../fastqc/fastqc_SAMPLE=ATAC_D0_rep2.err | 71 -------- .../fastqc/fastqc_SAMPLE=ATAC_D0_rep2.out | 0 .../fastqc/fastqc_SAMPLE=ATAC_D0_rep3.err | 71 -------- .../fastqc/fastqc_SAMPLE=ATAC_D0_rep3.out | 0 .../fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.err | 71 -------- .../fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.out | 0 .../fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.err | 71 -------- .../fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.out | 0 .../fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.err | 71 -------- .../fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.out | 0 .../fastqc/fastqc_SAMPLE=ATAC_D6_rep1.err | 71 -------- .../fastqc/fastqc_SAMPLE=ATAC_D6_rep1.out | 0 .../fastqc/fastqc_SAMPLE=ATAC_D6_rep2.err | 71 -------- .../fastqc/fastqc_SAMPLE=ATAC_D6_rep2.out | 0 .../fastqc/fastqc_SAMPLE=ATAC_D6_rep3.err | 71 -------- .../fastqc/fastqc_SAMPLE=ATAC_D6_rep3.out | 0 .../fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.err | 51 ------ .../fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.out | 0 .../fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.err | 51 ------ .../fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.out | 0 .../fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.err | 51 ------ .../fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.out | 0 .../fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.err | 51 ------ .../fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.out | 0 .../fastqc_SAMPLE=INPUT_shCtrl_Rep1.err | 51 ------ .../fastqc_SAMPLE=INPUT_shCtrl_Rep1.out | 0 .../fastqc_SAMPLE=INPUT_shCtrl_Rep2.err | 51 ------ .../fastqc_SAMPLE=INPUT_shCtrl_Rep2.out | 0 .../fastqc_SAMPLE=INPUT_shUbc9_Rep1.err | 51 ------ .../fastqc_SAMPLE=INPUT_shUbc9_Rep1.out | 0 .../fastqc_SAMPLE=INPUT_shUbc9_Rep2.err | 51 ------ .../fastqc_SAMPLE=INPUT_shUbc9_Rep2.out | 0 .../fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.err | 51 ------ .../fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.out | 0 .../fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.err | 51 ------ .../fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.out | 0 .../fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.err | 51 ------ .../fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.out | 0 .../fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.err | 51 ------ .../fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.out | 0 ...ts_CALLER=genrich.MOD=narrow.MARK=ATAC.err | 30 ---- ...ts_CALLER=genrich.MOD=narrow.MARK=ATAC.out | 0 ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err | 30 ---- ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out | 0 ...ounts_CALLER=macs2_narrow.MARK=H3K27ac.err | 32 ---- ...ounts_CALLER=macs2_narrow.MARK=H3K27ac.out | 0 ...e_counts_CALLER=macs2_narrow.MARK=Klf4.err | 32 ---- ...e_counts_CALLER=macs2_narrow.MARK=Klf4.out | 0 ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.err | 30 ---- ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.out | 0 .../genrich/genrich_SAMPLE=ATAC_D0_rep1.err | 47 ----- .../genrich/genrich_SAMPLE=ATAC_D0_rep1.out | 0 .../genrich/genrich_SAMPLE=ATAC_D0_rep2.err | 47 ----- .../genrich/genrich_SAMPLE=ATAC_D0_rep2.out | 0 .../genrich/genrich_SAMPLE=ATAC_D0_rep3.err | 47 ----- .../genrich/genrich_SAMPLE=ATAC_D0_rep3.out | 0 .../genrich/genrich_SAMPLE=ATAC_D6F_rep1.err | 47 ----- .../genrich/genrich_SAMPLE=ATAC_D6F_rep1.out | 0 .../genrich/genrich_SAMPLE=ATAC_D6F_rep2.err | 47 ----- .../genrich/genrich_SAMPLE=ATAC_D6F_rep2.out | 0 .../genrich/genrich_SAMPLE=ATAC_D6F_rep3.err | 47 ----- .../genrich/genrich_SAMPLE=ATAC_D6F_rep3.out | 0 .../genrich/genrich_SAMPLE=ATAC_D6_rep1.err | 47 ----- .../genrich/genrich_SAMPLE=ATAC_D6_rep1.out | 0 .../genrich/genrich_SAMPLE=ATAC_D6_rep2.err | 47 ----- .../genrich/genrich_SAMPLE=ATAC_D6_rep2.out | 0 .../genrich/genrich_SAMPLE=ATAC_D6_rep3.err | 47 ----- .../genrich/genrich_SAMPLE=ATAC_D6_rep3.out | 0 logs/slurm/igv_session/igv_session_unique.err | 27 --- logs/slurm/igv_session/igv_session_unique.out | 0 ...narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err | 55 ------ ...narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.out | 0 ...narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.err | 55 ------ ...narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.out | 0 ...narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.err | 55 ------ ...narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.out | 0 ...narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err | 55 ------ ...narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.out | 0 ...narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.err | 61 ------- ...narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.out | 0 ...narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.err | 61 ------- ...narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.out | 0 ...narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.err | 61 ------- ...narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.out | 0 ...narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.err | 61 ------- ...narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.out | 0 ...s2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.err | 61 ------- ...s2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.out | 0 ...s2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.err | 61 ------- ...s2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.out | 0 ...s2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.err | 61 ------- ...s2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.out | 0 ...s2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.err | 61 ------- ...s2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.out | 0 ...oModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.err | 55 ------ ...oModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.out | 0 ...oModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.err | 55 ------ ...oModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.out | 0 ...oModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.err | 55 ------ ...oModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.out | 0 ...e_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.err | 31 ---- ...e_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.out | 0 ...e_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.err | 31 ---- ...e_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.out | 0 ...e_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.err | 31 ---- ...e_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.out | 0 ..._metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.err | 31 ---- ..._metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.out | 0 ..._metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.err | 31 ---- ..._metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.out | 0 ..._metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.err | 31 ---- ..._metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.out | 0 ...e_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.err | 31 ---- ...e_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.out | 0 ...e_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.err | 31 ---- ...e_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.out | 0 ...e_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.err | 31 ---- ...e_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.out | 0 ...LER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.err | 39 ----- ...LER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.out | 0 ...LER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.err | 39 ----- ...LER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.out | 0 ...CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.err | 39 ----- ...CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.out | 0 ...CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.err | 39 ----- ...CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.out | 0 .../lanceotron_SAMPLE=ATAC_D0_rep1.err | 35 ---- .../lanceotron_SAMPLE=ATAC_D0_rep1.out | 0 .../lanceotron_SAMPLE=ATAC_D0_rep2.err | 35 ---- .../lanceotron_SAMPLE=ATAC_D0_rep2.out | 0 .../lanceotron_SAMPLE=ATAC_D0_rep3.err | 35 ---- .../lanceotron_SAMPLE=ATAC_D0_rep3.out | 0 .../lanceotron_SAMPLE=ATAC_D6F_rep1.err | 35 ---- .../lanceotron_SAMPLE=ATAC_D6F_rep1.out | 0 .../lanceotron_SAMPLE=ATAC_D6F_rep2.err | 35 ---- .../lanceotron_SAMPLE=ATAC_D6F_rep2.out | 0 .../lanceotron_SAMPLE=ATAC_D6F_rep3.err | 35 ---- .../lanceotron_SAMPLE=ATAC_D6F_rep3.out | 0 .../lanceotron_SAMPLE=ATAC_D6_rep1.err | 35 ---- .../lanceotron_SAMPLE=ATAC_D6_rep1.out | 0 .../lanceotron_SAMPLE=ATAC_D6_rep2.err | 35 ---- .../lanceotron_SAMPLE=ATAC_D6_rep2.out | 0 .../lanceotron_SAMPLE=ATAC_D6_rep3.err | 35 ---- .../lanceotron_SAMPLE=ATAC_D6_rep3.out | 0 .../macs2_SAMPLE=H3K27ac_shCtrl_PPR1.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shCtrl_PPR1.out | 0 .../macs2_SAMPLE=H3K27ac_shCtrl_PPR2.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shCtrl_PPR2.out | 0 .../macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.out | 0 .../macs2_SAMPLE=H3K27ac_shCtrl_Rep1.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shCtrl_Rep1.out | 0 .../macs2_SAMPLE=H3K27ac_shCtrl_Rep2.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shCtrl_Rep2.out | 0 .../macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.out | 0 .../macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.out | 0 .../macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.out | 0 .../macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.out | 0 .../macs2_SAMPLE=H3K27ac_shUbc9_PPR1.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shUbc9_PPR1.out | 0 .../macs2_SAMPLE=H3K27ac_shUbc9_PPR2.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shUbc9_PPR2.out | 0 .../macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.out | 0 .../macs2_SAMPLE=H3K27ac_shUbc9_Rep1.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shUbc9_Rep1.out | 0 .../macs2_SAMPLE=H3K27ac_shUbc9_Rep2.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shUbc9_Rep2.out | 0 .../macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.out | 0 .../macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.out | 0 .../macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.out | 0 .../macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.err | 49 ------ .../macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.out | 0 .../macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.out | 0 .../macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.out | 0 .../macs2_SAMPLE=Klf4_shCtrl_PPRPool.err | 49 ------ .../macs2_SAMPLE=Klf4_shCtrl_PPRPool.out | 0 .../macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.out | 0 .../macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.out | 0 .../macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.out | 0 .../macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.out | 0 .../macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.out | 0 .../macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.out | 0 .../macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.out | 0 .../macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.out | 0 .../macs2_SAMPLE=Klf4_shUbc9_PPRPool.err | 49 ------ .../macs2_SAMPLE=Klf4_shUbc9_PPRPool.out | 0 .../macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.out | 0 .../macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.out | 0 .../macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.out | 0 .../macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.out | 0 .../macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.out | 0 .../macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.err | 49 ------ .../macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.out | 0 .../macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.err | 53 ------ .../macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.out | 0 .../macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.err | 53 ------ .../macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.out | 0 .../macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.err | 53 ------ .../macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.out | 0 .../macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.err | 53 ------ .../macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.out | 0 .../macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.err | 53 ------ .../macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.out | 0 .../macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.err | 53 ------ .../macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.out | 0 .../macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.err | 53 ------ .../macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.out | 0 .../macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.err | 53 ------ .../macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.out | 0 .../macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.err | 53 ------ .../macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.out | 0 ...uplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.err | 30 ---- ...uplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.out | 0 ...uplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.err | 30 ---- ...uplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.out | 0 ...uplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.err | 30 ---- ...uplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.out | 0 ...plicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.err | 30 ---- ...plicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.out | 0 ...plicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.err | 30 ---- ...plicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.out | 0 ...plicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.err | 30 ---- ...plicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.out | 0 ...uplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.err | 30 ---- ...uplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.out | 0 ...uplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.err | 30 ---- ...uplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.out | 0 ...uplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.err | 30 ---- ...uplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.out | 0 ...es_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err | 32 ---- ...es_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out | 1 - ...es_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err | 32 ---- ...es_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out | 0 ...es_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err | 32 ---- ...es_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out | 1 - ...es_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err | 32 ---- ...es_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out | 0 ...es_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err | 32 ---- ...es_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out | 1 - ...es_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err | 32 ---- ...es_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out | 0 ...es_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err | 32 ---- ...es_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out | 1 - ...es_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err | 32 ---- ...es_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out | 0 ...ates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err | 32 ---- ...ates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out | 1 - ...ates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err | 32 ---- ...ates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out | 0 ...ates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err | 32 ---- ...ates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out | 1 - ...ates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err | 32 ---- ...ates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out | 0 ...ates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err | 32 ---- ...ates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out | 1 - ...ates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err | 32 ---- ...ates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out | 0 ...ates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err | 32 ---- ...ates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out | 1 - ...ates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err | 32 ---- ...ates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out | 0 ...cates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err | 32 ---- ...cates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out | 1 - ...cates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err | 32 ---- ...cates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out | 0 ...cates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err | 32 ---- ...cates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out | 1 - ...cates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err | 32 ---- ...cates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out | 0 ...cates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err | 32 ---- ...cates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out | 1 - ...cates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err | 32 ---- ...cates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out | 0 ...cates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err | 32 ---- ...cates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out | 1 - ...cates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err | 32 ---- ...cates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out | 0 ...caller_SAMPLE=ATAC_D0_rep1.FORM=narrow.err | 40 ----- ...caller_SAMPLE=ATAC_D0_rep1.FORM=narrow.out | 0 ...caller_SAMPLE=ATAC_D0_rep2.FORM=narrow.err | 40 ----- ...caller_SAMPLE=ATAC_D0_rep2.FORM=narrow.out | 0 ...caller_SAMPLE=ATAC_D0_rep3.FORM=narrow.err | 40 ----- ...caller_SAMPLE=ATAC_D0_rep3.FORM=narrow.out | 0 ...aller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.err | 40 ----- ...aller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.out | 0 ...aller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.err | 40 ----- ...aller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.out | 0 ...aller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.err | 40 ----- ...aller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.out | 0 ...caller_SAMPLE=ATAC_D6_rep1.FORM=narrow.err | 40 ----- ...caller_SAMPLE=ATAC_D6_rep1.FORM=narrow.out | 0 ...caller_SAMPLE=ATAC_D6_rep2.FORM=narrow.err | 40 ----- ...caller_SAMPLE=ATAC_D6_rep2.FORM=narrow.out | 0 ...caller_SAMPLE=ATAC_D6_rep3.FORM=narrow.err | 40 ----- ...caller_SAMPLE=ATAC_D6_rep3.FORM=narrow.out | 0 ..._CALLER=genrich.MOD=narrow.FORM=narrow.err | 41 ----- ..._CALLER=genrich.MOD=narrow.FORM=narrow.out | 0 ...LLER=lanceOtron.MOD=narrow.FORM=narrow.err | 41 ----- ...LLER=lanceOtron.MOD=narrow.FORM=narrow.out | 0 ...macs3_CallPeak.MOD=noModel.FORM=narrow.err | 41 ----- ...macs3_CallPeak.MOD=noModel.FORM=narrow.out | 0 .../metrics_chipr/metrics_chipr_unique.err | 26 --- .../metrics_chipr/metrics_chipr_unique.out | 0 .../metrics_peaks/metrics_peaks_unique.err | 27 --- .../metrics_peaks/metrics_peaks_unique.out | 0 logs/slurm/multiqc/multiqc_unique.err | 29 ---- logs/slurm/multiqc/multiqc_unique.out | 0 ...plotFingerprint_IP=H3K27ac_shCtrl_Rep1.err | 41 ----- ...plotFingerprint_IP=H3K27ac_shCtrl_Rep1.out | 0 ...plotFingerprint_IP=H3K27ac_shCtrl_Rep2.err | 41 ----- ...plotFingerprint_IP=H3K27ac_shCtrl_Rep2.out | 0 ...plotFingerprint_IP=H3K27ac_shUbc9_Rep1.err | 41 ----- ...plotFingerprint_IP=H3K27ac_shUbc9_Rep1.out | 0 ...plotFingerprint_IP=H3K27ac_shUbc9_Rep2.err | 41 ----- ...plotFingerprint_IP=H3K27ac_shUbc9_Rep2.out | 0 .../plotFingerprint_IP=Klf4_shCtrl_Rep1.err | 41 ----- .../plotFingerprint_IP=Klf4_shCtrl_Rep1.out | 0 .../plotFingerprint_IP=Klf4_shCtrl_Rep2.err | 41 ----- .../plotFingerprint_IP=Klf4_shCtrl_Rep2.out | 0 .../plotFingerprint_IP=Klf4_shUbc9_Rep1.err | 41 ----- .../plotFingerprint_IP=Klf4_shUbc9_Rep1.out | 0 .../plotFingerprint_IP=Klf4_shUbc9_Rep2.err | 41 ----- .../plotFingerprint_IP=Klf4_shUbc9_Rep2.out | 0 ...ap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err | 32 ---- ...ap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out | 0 ...ap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err | 32 ---- ...ap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out | 0 ...ap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err | 32 ---- ...ap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out | 0 ...ap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err | 32 ---- ...ap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out | 0 ...tmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err | 32 ---- ...tmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out | 0 ...tmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err | 32 ---- ...tmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out | 0 ...tmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err | 32 ---- ...tmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out | 0 ...tmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err | 32 ---- ...tmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out | 0 ...atmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err | 32 ---- ...atmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out | 0 ...atmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err | 32 ---- ...atmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out | 0 ...atmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err | 32 ---- ...atmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out | 0 ...atmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err | 32 ---- ...atmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out | 0 .../preIDR_PPR_IP=H3K27ac_shCtrl.err | 152 ----------------- .../preIDR_PPR_IP=H3K27ac_shCtrl.out | 0 .../preIDR_PPR_IP=H3K27ac_shUbc9.err | 152 ----------------- .../preIDR_PPR_IP=H3K27ac_shUbc9.out | 0 .../preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.err | 152 ----------------- .../preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.out | 0 .../preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.err | 152 ----------------- .../preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.out | 0 .../preIDR_SPR_IP=H3K27ac_shCtrl.err | 161 ------------------ .../preIDR_SPR_IP=H3K27ac_shCtrl.out | 0 .../preIDR_SPR_IP=H3K27ac_shUbc9.err | 161 ------------------ .../preIDR_SPR_IP=H3K27ac_shUbc9.out | 0 .../preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.err | 161 ------------------ .../preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.out | 0 .../preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.err | 161 ------------------ .../preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.out | 0 ...edRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.err | 30 ---- ...edRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.out | 0 ...edRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.err | 30 ---- ...edRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.out | 0 ...edRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.err | 30 ---- ...edRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.out | 0 ...dRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.err | 30 ---- ...dRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.out | 0 ...dRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.err | 30 ---- ...dRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.out | 0 ...dRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.err | 30 ---- ...dRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.out | 0 ...edRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.err | 30 ---- ...edRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.out | 0 ...edRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.err | 30 ---- ...edRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.out | 0 ...edRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.err | 30 ---- ...edRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.out | 0 ...ns_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err | 32 ---- ...ns_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out | 1 - ...ns_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err | 32 ---- ...ns_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out | 0 ...ns_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err | 32 ---- ...ns_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out | 1 - ...ns_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err | 32 ---- ...ns_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out | 0 ...ns_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err | 32 ---- ...ns_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out | 1 - ...ns_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err | 32 ---- ...ns_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out | 0 ...ns_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err | 32 ---- ...ns_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out | 1 - ...ns_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err | 32 ---- ...ns_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out | 0 ...ions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err | 32 ---- ...ions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out | 1 - ...ions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err | 32 ---- ...ions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out | 0 ...ions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err | 32 ---- ...ions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out | 1 - ...ions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err | 32 ---- ...ions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out | 0 ...ions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err | 32 ---- ...ions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out | 1 - ...ions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err | 32 ---- ...ions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out | 0 ...ions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err | 32 ---- ...ions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out | 1 - ...ions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err | 32 ---- ...ions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out | 0 ...gions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err | 32 ---- ...gions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out | 1 - ...gions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err | 32 ---- ...gions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out | 0 ...gions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err | 32 ---- ...gions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out | 1 - ...gions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err | 32 ---- ...gions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out | 0 ...gions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err | 32 ---- ...gions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out | 1 - ...gions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err | 32 ---- ...gions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out | 0 ...gions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err | 32 ---- ...gions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out | 1 - ...gions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err | 32 ---- ...gions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out | 0 ...DR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.err | 61 ------- ...DR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.out | 0 ...shCtrl.CONSENSUS_MOD=select.narrowPeak.err | 61 ------- ...shCtrl.CONSENSUS_MOD=select.narrowPeak.out | 0 ...shUbc9.CONSENSUS_MOD=select.narrowPeak.err | 61 ------- ...shUbc9.CONSENSUS_MOD=select.narrowPeak.out | 0 ...shCtrl.CONSENSUS_MOD=select.narrowPeak.err | 61 ------- ...shCtrl.CONSENSUS_MOD=select.narrowPeak.out | 0 ...shUbc9.CONSENSUS_MOD=select.narrowPeak.err | 61 ------- ...shUbc9.CONSENSUS_MOD=select.narrowPeak.out | 0 ...aks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.err | 35 ---- ...aks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.out | 0 ...aks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.err | 41 ----- ...aks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.out | 1 - ..._peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.err | 41 ----- ..._peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.out | 1 - ..._peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.err | 41 ----- ..._peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.out | 1 - .../slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.err | 32 ---- .../slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.out | 0 .../slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.err | 32 ---- .../slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.out | 0 .../slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.err | 32 ---- .../slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.out | 0 .../slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.err | 32 ---- .../slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.out | 0 logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.err | 32 ---- logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.out | 0 logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.err | 32 ---- logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.out | 0 logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.err | 32 ---- logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.out | 0 logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.err | 32 ---- logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.out | 0 logs/slurm/stats_IA/stats_IA_unique.err | 27 --- logs/slurm/stats_IA/stats_IA_unique.out | 0 ..._CALLER=genrich.MOD=narrow.FORM=narrow.err | 26 --- ..._CALLER=genrich.MOD=narrow.FORM=narrow.out | 0 ...LLER=lanceOtron.MOD=narrow.FORM=narrow.err | 26 --- ...LLER=lanceOtron.MOD=narrow.FORM=narrow.out | 0 ...ts_peakCalling_CALLER=macs2.MOD=narrow.err | 28 --- ...ts_peakCalling_CALLER=macs2.MOD=narrow.out | 0 ...macs3_CallPeak.MOD=noModel.FORM=narrow.err | 26 --- ...macs3_CallPeak.MOD=noModel.FORM=narrow.out | 0 ...ks_CALLER=genrich.MOD=narrow.MARK=ATAC.err | 35 ---- ...ks_CALLER=genrich.MOD=narrow.MARK=ATAC.out | 0 ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err | 35 ---- ...CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out | 0 ...peaks_CALLER=macs2_narrow.MARK=H3K27ac.err | 38 ----- ...peaks_CALLER=macs2_narrow.MARK=H3K27ac.out | 0 ...on_peaks_CALLER=macs2_narrow.MARK=Klf4.err | 38 ----- ...on_peaks_CALLER=macs2_narrow.MARK=Klf4.out | 0 ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.err | 35 ---- ...R=macs3_CallPeak.MOD=noModel.MARK=ATAC.out | 0 singularity/.gitkeep | 0 singularity/epeak.def | 131 -------------- 836 files changed, 18800 deletions(-) delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.err delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.out delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.err delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.out delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.err delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.out delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.err delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.out delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.err delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.out delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.err delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.out delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.err delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.out delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.err delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.out delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.err delete mode 100644 logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep1.err delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep1.out delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep2.err delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep2.out delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep3.err delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep3.out delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.err delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.out delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.err delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.out delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.err delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.out delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep1.err delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep1.out delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep2.err delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep2.out delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep3.err delete mode 100644 logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep3.out delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=genrich.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=genrich.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=H3K27ac.err delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=H3K27ac.out delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=Klf4.err delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=Klf4.out delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err delete mode 100644 logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.err delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.out delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.err delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.out delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err delete mode 100644 logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out delete mode 100644 logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=H3K27ac.err delete mode 100644 logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=H3K27ac.out delete mode 100644 logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=Klf4.err delete mode 100644 logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=Klf4.out delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=genrich.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=genrich.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=H3K27ac.err delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=H3K27ac.out delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=Klf4.err delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=Klf4.out delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err delete mode 100644 logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shCtrl.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shCtrl.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shUbc9.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shUbc9.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shCtrl.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shCtrl.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shUbc9.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shUbc9.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D0.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D0.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6.out delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6F.err delete mode 100644 logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6F.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..out delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..err delete mode 100644 logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.out delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.err delete mode 100644 logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.out delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.err delete mode 100644 logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.out delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=genrich.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=genrich.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=H3K27ac.err delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=H3K27ac.out delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=Klf4.err delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=Klf4.out delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err delete mode 100644 logs/slurm/feature_counts/feature_counts_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.err delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.out delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.err delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.out delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.err delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.out delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.err delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.out delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.err delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.out delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.err delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.out delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.err delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.out delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.err delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.out delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.err delete mode 100644 logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.out delete mode 100644 logs/slurm/igv_session/igv_session_unique.err delete mode 100644 logs/slurm/igv_session/igv_session_unique.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=genrich.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=genrich.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.out delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.err delete mode 100644 logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.out delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.err delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.out delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.err delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.out delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.err delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.out delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.err delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.out delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.err delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.out delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.err delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.out delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.err delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.out delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.err delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.out delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.err delete mode 100644 logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.out delete mode 100644 logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.err delete mode 100644 logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.out delete mode 100644 logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.err delete mode 100644 logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.out delete mode 100644 logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.err delete mode 100644 logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.out delete mode 100644 logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.err delete mode 100644 logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.out delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.err delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.out delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.err delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.out delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.err delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.out delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.err delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.out delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.err delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.out delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.err delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.out delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.err delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.out delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.err delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.out delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.err delete mode 100644 logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.out delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.err delete mode 100644 logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.out delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.err delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.out delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.err delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.out delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.err delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.out delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.err delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.out delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.err delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.out delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.err delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.out delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.err delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.out delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.err delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.out delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.err delete mode 100644 logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep1.FORM=narrow.err delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep1.FORM=narrow.out delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep2.FORM=narrow.err delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep2.FORM=narrow.out delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep3.FORM=narrow.err delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep3.FORM=narrow.out delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.err delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.out delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.err delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.out delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.err delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.out delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep1.FORM=narrow.err delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep1.FORM=narrow.out delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep2.FORM=narrow.err delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep2.FORM=narrow.out delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep3.FORM=narrow.err delete mode 100644 logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep3.FORM=narrow.out delete mode 100644 logs/slurm/metrics_chipr/metrics_chipr_CALLER=genrich.MOD=narrow.FORM=narrow.err delete mode 100644 logs/slurm/metrics_chipr/metrics_chipr_CALLER=genrich.MOD=narrow.FORM=narrow.out delete mode 100644 logs/slurm/metrics_chipr/metrics_chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err delete mode 100644 logs/slurm/metrics_chipr/metrics_chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.out delete mode 100644 logs/slurm/metrics_chipr/metrics_chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err delete mode 100644 logs/slurm/metrics_chipr/metrics_chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.out delete mode 100644 logs/slurm/metrics_chipr/metrics_chipr_unique.err delete mode 100644 logs/slurm/metrics_chipr/metrics_chipr_unique.out delete mode 100644 logs/slurm/metrics_peaks/metrics_peaks_unique.err delete mode 100644 logs/slurm/metrics_peaks/metrics_peaks_unique.out delete mode 100644 logs/slurm/multiqc/multiqc_unique.err delete mode 100644 logs/slurm/multiqc/multiqc_unique.out delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.err delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.out delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.err delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.out delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.err delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.out delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.err delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.out delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.err delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.out delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.err delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.out delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.err delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.out delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.err delete mode 100644 logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.err delete mode 100644 logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.out delete mode 100644 logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.err delete mode 100644 logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.out delete mode 100644 logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.err delete mode 100644 logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.out delete mode 100644 logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.err delete mode 100644 logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.out delete mode 100644 logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.err delete mode 100644 logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.out delete mode 100644 logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.err delete mode 100644 logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.out delete mode 100644 logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.err delete mode 100644 logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.out delete mode 100644 logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.err delete mode 100644 logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err delete mode 100644 logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.err delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.out delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=select.narrowPeak.err delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=select.narrowPeak.out delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CONSENSUS_MOD=select.narrowPeak.err delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CONSENSUS_MOD=select.narrowPeak.out delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CONSENSUS_MOD=select.narrowPeak.err delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CONSENSUS_MOD=select.narrowPeak.out delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CONSENSUS_MOD=select.narrowPeak.err delete mode 100644 logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CONSENSUS_MOD=select.narrowPeak.out delete mode 100644 logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.err delete mode 100644 logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.out delete mode 100644 logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.err delete mode 100644 logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.out delete mode 100644 logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.err delete mode 100644 logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.out delete mode 100644 logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.err delete mode 100644 logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.out delete mode 100644 logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.err delete mode 100644 logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.out delete mode 100644 logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.err delete mode 100644 logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.out delete mode 100644 logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.err delete mode 100644 logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.out delete mode 100644 logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.err delete mode 100644 logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.out delete mode 100644 logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.err delete mode 100644 logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.out delete mode 100644 logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.err delete mode 100644 logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.out delete mode 100644 logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.err delete mode 100644 logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.out delete mode 100644 logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.err delete mode 100644 logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.out delete mode 100644 logs/slurm/stats_IA/stats_IA_unique.err delete mode 100644 logs/slurm/stats_IA/stats_IA_unique.out delete mode 100644 logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=genrich.MOD=narrow.FORM=narrow.err delete mode 100644 logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=genrich.MOD=narrow.FORM=narrow.out delete mode 100644 logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err delete mode 100644 logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=lanceOtron.MOD=narrow.FORM=narrow.out delete mode 100644 logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs2.MOD=narrow.err delete mode 100644 logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs2.MOD=narrow.out delete mode 100644 logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err delete mode 100644 logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.out delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=genrich.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=genrich.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=H3K27ac.err delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=H3K27ac.out delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=Klf4.err delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=Klf4.out delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err delete mode 100644 logs/slurm/union_peaks/union_peaks_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out delete mode 100644 singularity/.gitkeep delete mode 100644 singularity/epeak.def diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.err b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.err deleted file mode 100644 index be94c45..0000000 --- a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12025, disk_mib=11468, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:27:45 2024] -localrule EstimateLibraryComplexity: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/Complexity/ATAC_D0_rep1_hg38_metrics.txt - log: RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep1_hg38_complexity.out, RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep1_hg38_complexity.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=12025, disk_mib=11468, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard EstimateLibraryComplexity I=RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/Complexity/ATAC_D0_rep1_hg38_metrics.txt TMP_DIR=$TMPDIR > RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep1_hg38_complexity.out 2> RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep1_hg38_complexity.err - -Activating singularity image epeak.sif -[Thu Sep 12 11:37:38 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.out b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.err b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.err deleted file mode 100644 index 0bdeae9..0000000 --- a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10754, disk_mib=10256, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:30:45 2024] -localrule EstimateLibraryComplexity: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/Complexity/ATAC_D0_rep2_hg38_metrics.txt - log: RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep2_hg38_complexity.out, RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep2_hg38_complexity.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=10754, disk_mib=10256, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard EstimateLibraryComplexity I=RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/Complexity/ATAC_D0_rep2_hg38_metrics.txt TMP_DIR=$TMPDIR > RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep2_hg38_complexity.out 2> RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep2_hg38_complexity.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:38:31 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.out b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.err b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.err deleted file mode 100644 index 44c2706..0000000 --- a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9524, disk_mib=9083, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 07:47:48 2024] -localrule EstimateLibraryComplexity: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/Complexity/ATAC_D0_rep3_hg38_metrics.txt - log: RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep3_hg38_complexity.out, RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep3_hg38_complexity.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=9524, disk_mib=9083, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard EstimateLibraryComplexity I=RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/Complexity/ATAC_D0_rep3_hg38_metrics.txt TMP_DIR=$TMPDIR > RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep3_hg38_complexity.out 2> RES_ATAC/05-QC/Complexity/logs/ATAC_D0_rep3_hg38_complexity.err - -Activating singularity image epeak.sif -[Thu Sep 12 07:54:56 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.out b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.err b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.err deleted file mode 100644 index 4c0b491..0000000 --- a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5065, disk_mb=5310, disk_mib=5065, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:52:51 2024] -localrule EstimateLibraryComplexity: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/Complexity/ATAC_D6F_rep1_hg38_metrics.txt - log: RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep1_hg38_complexity.out, RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep1_hg38_complexity.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=5065, disk_mb=5310, disk_mib=5065, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard EstimateLibraryComplexity I=RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/Complexity/ATAC_D6F_rep1_hg38_metrics.txt TMP_DIR=$TMPDIR > RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep1_hg38_complexity.out 2> RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep1_hg38_complexity.err - -Activating singularity image epeak.sif -[Thu Sep 12 00:56:34 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.out b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.err b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.err deleted file mode 100644 index 7c6c3dc..0000000 --- a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5250, disk_mb=5504, disk_mib=5250, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:54:49 2024] -localrule EstimateLibraryComplexity: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/Complexity/ATAC_D6F_rep2_hg38_metrics.txt - log: RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep2_hg38_complexity.out, RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep2_hg38_complexity.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=5250, disk_mb=5504, disk_mib=5250, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard EstimateLibraryComplexity I=RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/Complexity/ATAC_D6F_rep2_hg38_metrics.txt TMP_DIR=$TMPDIR > RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep2_hg38_complexity.out 2> RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep2_hg38_complexity.err - -Activating singularity image epeak.sif -[Wed Sep 11 23:58:44 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.out b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.err b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.err deleted file mode 100644 index 81170c9..0000000 --- a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6182, disk_mb=6482, disk_mib=6182, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 02:11:50 2024] -localrule EstimateLibraryComplexity: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/Complexity/ATAC_D6F_rep3_hg38_metrics.txt - log: RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep3_hg38_complexity.out, RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep3_hg38_complexity.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3, REF=hg38 - resources: mem_mb=9537, mem_mib=6182, disk_mb=6482, disk_mib=6182, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard EstimateLibraryComplexity I=RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/Complexity/ATAC_D6F_rep3_hg38_metrics.txt TMP_DIR=$TMPDIR > RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep3_hg38_complexity.out 2> RES_ATAC/05-QC/Complexity/logs/ATAC_D6F_rep3_hg38_complexity.err - -Activating singularity image epeak.sif -[Thu Sep 12 02:16:40 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.out b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.err b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.err deleted file mode 100644 index 3d44b62..0000000 --- a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5709, disk_mb=5986, disk_mib=5709, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:25:43 2024] -localrule EstimateLibraryComplexity: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/Complexity/ATAC_D6_rep1_hg38_metrics.txt - log: RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep1_hg38_complexity.out, RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep1_hg38_complexity.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=5709, disk_mb=5986, disk_mib=5709, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard EstimateLibraryComplexity I=RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/Complexity/ATAC_D6_rep1_hg38_metrics.txt TMP_DIR=$TMPDIR > RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep1_hg38_complexity.out 2> RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep1_hg38_complexity.err - -Activating singularity image epeak.sif -[Thu Sep 12 00:29:48 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.out b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.err b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.err deleted file mode 100644 index b31b25f..0000000 --- a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7497, disk_mb=7861, disk_mib=7497, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 05:16:44 2024] -localrule EstimateLibraryComplexity: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/Complexity/ATAC_D6_rep2_hg38_metrics.txt - log: RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep2_hg38_complexity.out, RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep2_hg38_complexity.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=7497, disk_mb=7861, disk_mib=7497, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard EstimateLibraryComplexity I=RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/Complexity/ATAC_D6_rep2_hg38_metrics.txt TMP_DIR=$TMPDIR > RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep2_hg38_complexity.out 2> RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep2_hg38_complexity.err - -Activating singularity image epeak.sif -[Thu Sep 12 05:22:58 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.out b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.err b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.err deleted file mode 100644 index 7a9a33f..0000000 --- a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5850, disk_mb=6134, disk_mib=5850, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:17:44 2024] -localrule EstimateLibraryComplexity: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/Complexity/ATAC_D6_rep3_hg38_metrics.txt - log: RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep3_hg38_complexity.out, RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep3_hg38_complexity.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3, REF=hg38 - resources: mem_mb=9537, mem_mib=5850, disk_mb=6134, disk_mib=5850, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard EstimateLibraryComplexity I=RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/Complexity/ATAC_D6_rep3_hg38_metrics.txt TMP_DIR=$TMPDIR > RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep3_hg38_complexity.out 2> RES_ATAC/05-QC/Complexity/logs/ATAC_D6_rep3_hg38_complexity.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:22:09 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.out b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.err deleted file mode 100644 index 3c40126..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.err +++ /dev/null @@ -1,36 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=24051, disk_mib=22937, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:27:45 2024] -localrule bamCoverage: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/12-IGV/ATAC_D0_rep1_hg38_coverage.bw - log: RES_ATAC/12-IGV/logs/ATAC_D0_rep1_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=24051, disk_mib=22937, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam && RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]]; then - S=$(cat RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D0_rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D0_rep1_hg38.out - else - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D0_rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D0_rep1_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 11:59:21 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.err deleted file mode 100644 index ef4ec03..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.err +++ /dev/null @@ -1,36 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=21509, disk_mib=20513, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:30:45 2024] -localrule bamCoverage: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/12-IGV/ATAC_D0_rep2_hg38_coverage.bw - log: RES_ATAC/12-IGV/logs/ATAC_D0_rep2_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=21509, disk_mib=20513, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam && RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]]; then - S=$(cat RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D0_rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D0_rep2_hg38.out - else - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D0_rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D0_rep2_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 10:58:35 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.err deleted file mode 100644 index dc8c82c..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.err +++ /dev/null @@ -1,36 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=19048, disk_mib=18166, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 07:47:48 2024] -localrule bamCoverage: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/12-IGV/ATAC_D0_rep3_hg38_coverage.bw - log: RES_ATAC/12-IGV/logs/ATAC_D0_rep3_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=19048, disk_mib=18166, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam && RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]]; then - S=$(cat RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D0_rep3_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D0_rep3_hg38.out - else - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D0_rep3_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D0_rep3_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 08:12:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.err deleted file mode 100644 index 1a45c1b..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.err +++ /dev/null @@ -1,36 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=10620, disk_mib=10129, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:52:51 2024] -localrule bamCoverage: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/12-IGV/ATAC_D6F_rep1_hg38_coverage.bw - log: RES_ATAC/12-IGV/logs/ATAC_D6F_rep1_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=10620, disk_mib=10129, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam && RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]]; then - S=$(cat RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6F_rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6F_rep1_hg38.out - else - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6F_rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6F_rep1_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 01:09:17 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.err deleted file mode 100644 index ecd0027..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.err +++ /dev/null @@ -1,36 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=11008, disk_mib=10499, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:54:49 2024] -localrule bamCoverage: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/12-IGV/ATAC_D6F_rep2_hg38_coverage.bw - log: RES_ATAC/12-IGV/logs/ATAC_D6F_rep2_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=11008, disk_mib=10499, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam && RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]]; then - S=$(cat RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6F_rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6F_rep2_hg38.out - else - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6F_rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6F_rep2_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 00:11:36 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.err deleted file mode 100644 index a94cff3..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.err +++ /dev/null @@ -1,36 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=12964, disk_mib=12364, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 02:11:50 2024] -localrule bamCoverage: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/12-IGV/ATAC_D6F_rep3_hg38_coverage.bw - log: RES_ATAC/12-IGV/logs/ATAC_D6F_rep3_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=12964, disk_mib=12364, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam && RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]]; then - S=$(cat RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6F_rep3_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6F_rep3_hg38.out - else - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6F_rep3_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6F_rep3_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 02:30:06 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.err deleted file mode 100644 index 739409d..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.err +++ /dev/null @@ -1,36 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=11973, disk_mib=11419, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:25:43 2024] -localrule bamCoverage: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/12-IGV/ATAC_D6_rep1_hg38_coverage.bw - log: RES_ATAC/12-IGV/logs/ATAC_D6_rep1_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=11973, disk_mib=11419, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam && RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]]; then - S=$(cat RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6_rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6_rep1_hg38.out - else - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6_rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6_rep1_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 00:43:01 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.err deleted file mode 100644 index b398866..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.err +++ /dev/null @@ -1,36 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=15723, disk_mib=14995, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 05:16:44 2024] -localrule bamCoverage: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/12-IGV/ATAC_D6_rep2_hg38_coverage.bw - log: RES_ATAC/12-IGV/logs/ATAC_D6_rep2_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=15723, disk_mib=14995, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam && RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]]; then - S=$(cat RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6_rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6_rep2_hg38.out - else - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6_rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6_rep2_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 05:38:17 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.err deleted file mode 100644 index dffd4c2..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.err +++ /dev/null @@ -1,36 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=12269, disk_mib=11701, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:17:44 2024] -localrule bamCoverage: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/12-IGV/ATAC_D6_rep3_hg38_coverage.bw - log: RES_ATAC/12-IGV/logs/ATAC_D6_rep3_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=12269, disk_mib=11701, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam && RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]]; then - S=$(cat RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6_rep3_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6_rep3_hg38.out - else - bamCoverage --bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam --outFileName RES_ATAC/12-IGV/ATAC_D6_rep3_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> RES_ATAC/12-IGV/logs/ATAC_D6_rep3_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 10:36:06 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index c62a8e5..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=9477, disk_mib=9038, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:48:55 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep1_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep1_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=9477, disk_mib=9038, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep1_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep1_hg38.out - fi - - -Activating singularity image epeak.sif -[Tue Aug 27 14:55:02 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 24bee8c..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=5094, disk_mb=5341, disk_mib=5094, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:21:07 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep1_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep1_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=mm10 - resources: mem_mb=19073, mem_mib=5094, disk_mb=5341, disk_mib=5094, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep1_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep1_mm10.out - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 21:34:09 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index 1eb284c..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=9979, disk_mib=9517, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:50:08 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep2_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep2_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=9979, disk_mib=9517, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep2_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep2_hg38.out - fi - - -Activating singularity image epeak.sif -[Tue Aug 27 14:56:06 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index 7c2021c..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=4788, disk_mb=5020, disk_mib=4788, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:20:11 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep2_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep2_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=mm10 - resources: mem_mb=19073, mem_mib=4788, disk_mb=5020, disk_mib=4788, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep2_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shCtrl_Rep2_mm10.out - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 22:32:58 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index 749020c..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=11279, disk_mib=10757, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Aug 28 14:20:03 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep1_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep1_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=11279, disk_mib=10757, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep1_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep1_hg38.out - fi - - -Activating singularity image epeak.sif -[Wed Aug 28 14:26:29 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index aeb4f7e..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=5177, disk_mb=5428, disk_mib=5177, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:48:15 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep1_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep1_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=mm10 - resources: mem_mb=19073, mem_mib=5177, disk_mb=5428, disk_mib=5177, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep1_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep1_mm10.out - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 22:01:27 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index 40ef0e3..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=8820, disk_mib=8412, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:54:58 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep2_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep2_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=8820, disk_mib=8412, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep2_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep2_hg38.out - fi - - -Activating singularity image epeak.sif -[Tue Aug 27 15:01:01 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 9c0ff81..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=4712, disk_mb=4940, disk_mib=4712, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 20:56:05 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep2_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep2_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=mm10 - resources: mem_mb=19073, mem_mib=4712, disk_mb=4940, disk_mib=4712, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep2_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/H3K27ac_shUbc9_Rep2_mm10.out - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 21:08:20 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index a4799c2..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=8196, disk_mib=7817, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 15:09:00 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep1_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep1_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=8196, disk_mib=7817, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep1_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep1_hg38.out - fi - - -Activating singularity image epeak.sif -[Tue Aug 27 15:14:59 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 70ab653..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=3784, disk_mb=3967, disk_mib=3784, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:06 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep1_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep1_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=mm10 - resources: mem_mb=19073, mem_mib=3784, disk_mb=3967, disk_mib=3784, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep1_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep1_mm10.out - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 23:15:50 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index e3e0d06..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=9378, disk_mib=8944, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Aug 29 11:00:04 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep2_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep2_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=9378, disk_mib=8944, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep2_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep2_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Aug 29 11:06:38 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index 54f5824..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=5381, disk_mb=5642, disk_mib=5381, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep2_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep2_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=mm10 - resources: mem_mb=19073, mem_mib=5381, disk_mb=5642, disk_mib=5381, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep2_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shCtrl_Rep2_mm10.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 11:18:09 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index ee0befb..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=9369, disk_mib=8935, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Aug 29 11:09:08 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep1_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep1_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=9369, disk_mib=8935, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep1_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep1_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Aug 29 11:15:08 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 04109dd..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=4825, disk_mb=5059, disk_mib=4825, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep1_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep1_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=mm10 - resources: mem_mb=19073, mem_mib=4825, disk_mb=5059, disk_mib=4825, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep1_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep1_mm10.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 11:16:11 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index 01d3a74..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=10044, disk_mib=9579, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Aug 29 11:10:09 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep2_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep2_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=10044, disk_mib=9579, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep2_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep2_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Aug 29 11:16:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index d1377ff..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=6153, disk_mb=6451, disk_mib=6153, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:05:42 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep2_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep2_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=mm10 - resources: mem_mb=19073, mem_mib=6153, disk_mb=6451, disk_mib=6153, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep2_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/INPUT_shUbc9_Rep2_mm10.out - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 11:20:21 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index a1430a6..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7535, disk_mb=7901, disk_mib=7535, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:41:02 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep1_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep1_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=hg38 - resources: mem_mb=19073, mem_mib=7535, disk_mb=7901, disk_mib=7535, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep1_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep1_hg38.out - fi - - -Activating singularity image epeak.sif -[Tue Aug 27 14:47:18 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index a2082f6..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=6800, disk_mb=7130, disk_mib=6800, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:30:11 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep1_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep1_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=mm10 - resources: mem_mb=19073, mem_mib=6800, disk_mb=7130, disk_mib=6800, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep1_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep1_mm10.out - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 21:47:14 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index c1e6fe1..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=6891, disk_mb=7225, disk_mib=6891, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:44:55 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep2_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep2_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=hg38 - resources: mem_mb=19073, mem_mib=6891, disk_mb=7225, disk_mib=6891, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep2_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep2_hg38.out - fi - - -Activating singularity image epeak.sif -[Tue Aug 27 14:50:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index 9aa2bda..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=6036, disk_mb=6329, disk_mib=6036, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 20:55:05 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep2_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep2_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=mm10 - resources: mem_mb=19073, mem_mib=6036, disk_mb=6329, disk_mib=6036, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep2_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shCtrl_Rep2_mm10.out - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 21:10:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index 0b9d8f7..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=8158, disk_mib=7781, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 15:03:54 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep1_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep1_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=8158, disk_mib=7781, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep1_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep1_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep1_hg38.out - fi - - -Activating singularity image epeak.sif -[Tue Aug 27 15:10:00 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index a5b0a5c..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=6921, disk_mb=7257, disk_mib=6921, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:47:10 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep1_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep1_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=mm10 - resources: mem_mb=19073, mem_mib=6921, disk_mb=7257, disk_mib=6921, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep1_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep1_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep1_mm10.out - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 23:04:37 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index e9276e8..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=9922, disk_mib=9463, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Aug 29 11:00:04 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep2_hg38_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep2_hg38.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=hg38 - resources: mem_mb=19073, mem_mib=7630, disk_mb=9922, disk_mib=9463, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep2_hg38.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep2_hg38_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep2_hg38.out - fi - - -Activating singularity image epeak.sif -[Thu Aug 29 11:06:40 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index ba14d08..0000000 --- a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=8990, disk_mib=8574, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:44:12 2024] -localrule bamCoverage: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep2_mm10_coverage.bw - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep2_mm10.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=mm10 - resources: mem_mb=19073, mem_mib=7630, disk_mb=8990, disk_mib=8574, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - if [[ -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam && /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam == *"_scaleFactor.txt"* ]] - then - S=$(cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam) - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --scaleFactor $S --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep2_mm10.out - else - bamCoverage --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --outFileName /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep2_mm10_coverage.bw --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/Klf4_shUbc9_Rep2_mm10.out - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 23:04:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep1.err deleted file mode 100644 index c0fcf6b..0000000 --- a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep1.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12025, disk_mib=11468, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:27:45 2024] -localrule bam_to_bigwig: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep1_dedup_sort.bw - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep1_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep1_dedup_sort.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1 - resources: mem_mb=9537, mem_mib=7630, disk_mb=12025, disk_mib=11468, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - bamCoverage -b RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep1_dedup_sort.bw > RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep1_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep1_dedup_sort.err - -Activating singularity image epeak.sif -[Thu Sep 12 11:49:35 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep1.out b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep2.err deleted file mode 100644 index 0dcfcdc..0000000 --- a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep2.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10754, disk_mib=10256, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:30:45 2024] -localrule bam_to_bigwig: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep2_dedup_sort.bw - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep2_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep2_dedup_sort.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=10754, disk_mib=10256, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - bamCoverage -b RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep2_dedup_sort.bw > RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep2_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep2_dedup_sort.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:49:38 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep2.out b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep3.err deleted file mode 100644 index bca3587..0000000 --- a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep3.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9524, disk_mib=9083, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 07:47:48 2024] -localrule bam_to_bigwig: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep3_dedup_sort.bw - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep3_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep3_dedup_sort.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3 - resources: mem_mb=9537, mem_mib=7630, disk_mb=9524, disk_mib=9083, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - bamCoverage -b RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep3_dedup_sort.bw > RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep3_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D0_rep3_dedup_sort.err - -Activating singularity image epeak.sif -[Thu Sep 12 08:04:45 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep3.out b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.err deleted file mode 100644 index 1e95780..0000000 --- a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5065, disk_mb=5310, disk_mib=5065, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:52:51 2024] -localrule bam_to_bigwig: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep1_dedup_sort.bw - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep1_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep1_dedup_sort.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1 - resources: mem_mb=9537, mem_mib=5065, disk_mb=5310, disk_mib=5065, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - bamCoverage -b RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep1_dedup_sort.bw > RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep1_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep1_dedup_sort.err - -Activating singularity image epeak.sif -[Thu Sep 12 01:03:08 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.out b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.err deleted file mode 100644 index d13adcb..0000000 --- a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5250, disk_mb=5504, disk_mib=5250, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:54:49 2024] -localrule bam_to_bigwig: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep2_dedup_sort.bw - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep2_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep2_dedup_sort.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2 - resources: mem_mb=9537, mem_mib=5250, disk_mb=5504, disk_mib=5250, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - bamCoverage -b RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep2_dedup_sort.bw > RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep2_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep2_dedup_sort.err - -Activating singularity image epeak.sif -[Thu Sep 12 00:05:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.out b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.err deleted file mode 100644 index 79a4068..0000000 --- a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6182, disk_mb=6482, disk_mib=6182, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 02:11:50 2024] -localrule bam_to_bigwig: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep3_dedup_sort.bw - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep3_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep3_dedup_sort.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3 - resources: mem_mb=9537, mem_mib=6182, disk_mb=6482, disk_mib=6182, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - bamCoverage -b RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep3_dedup_sort.bw > RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep3_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6F_rep3_dedup_sort.err - -Activating singularity image epeak.sif -[Thu Sep 12 02:23:42 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.out b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep1.err deleted file mode 100644 index a090b89..0000000 --- a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep1.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5709, disk_mb=5986, disk_mib=5709, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:25:43 2024] -localrule bam_to_bigwig: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep1_dedup_sort.bw - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep1_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep1_dedup_sort.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1 - resources: mem_mb=9537, mem_mib=5709, disk_mb=5986, disk_mib=5709, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - bamCoverage -b RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep1_dedup_sort.bw > RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep1_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep1_dedup_sort.err - -Activating singularity image epeak.sif -[Thu Sep 12 00:36:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep1.out b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep2.err deleted file mode 100644 index 980b238..0000000 --- a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep2.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7497, disk_mb=7861, disk_mib=7497, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 05:16:44 2024] -localrule bam_to_bigwig: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep2_dedup_sort.bw - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep2_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep2_dedup_sort.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2 - resources: mem_mb=9537, mem_mib=7497, disk_mb=7861, disk_mib=7497, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - bamCoverage -b RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep2_dedup_sort.bw > RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep2_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep2_dedup_sort.err - -Activating singularity image epeak.sif -[Thu Sep 12 05:31:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep2.out b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep3.err deleted file mode 100644 index 1265c4f..0000000 --- a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep3.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5850, disk_mb=6134, disk_mib=5850, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:17:46 2024] -localrule bam_to_bigwig: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep3_dedup_sort.bw - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep3_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep3_dedup_sort.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3 - resources: mem_mb=9537, mem_mib=5850, disk_mb=6134, disk_mib=5850, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - bamCoverage -b RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep3_dedup_sort.bw > RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep3_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/logs/ATAC_D6_rep3_dedup_sort.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:29:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep3.out b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=genrich.MOD=narrow.MARK=ATAC.err b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=genrich.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index 7bf8328..0000000 --- a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=genrich.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:27:00 2024] -localrule bed_to_gff: - input: RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed - output: RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff - log: RES_ATAC/09-CountMatrix/genrich_narrow/logs/ATAC_Optimal_Peaks_bed2gff.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - awk 'BEGIN{OFS=" "} {print $1" ChIPflow peak "$2+1" "$3+1" . . . gene_id "$1"_"$2"_"$3}' RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed > RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff 2> RES_ATAC/09-CountMatrix/genrich_narrow/logs/ATAC_Optimal_Peaks_bed2gff.out - - -Activating singularity image epeak.sif -[Thu Sep 12 12:27:01 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=genrich.MOD=narrow.MARK=ATAC.out b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=genrich.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index 44b6315..0000000 --- a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:58:56 2024] -localrule bed_to_gff: - input: RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed - output: RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff - log: RES_ATAC/09-CountMatrix/lanceOtron_narrow/logs/ATAC_Optimal_Peaks_bed2gff.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - awk 'BEGIN{OFS=" "} {print $1" ChIPflow peak "$2+1" "$3+1" . . . gene_id "$1"_"$2"_"$3}' RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed > RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff 2> RES_ATAC/09-CountMatrix/lanceOtron_narrow/logs/ATAC_Optimal_Peaks_bed2gff.out - - -Activating singularity image epeak.sif -[Thu Sep 12 12:58:56 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=H3K27ac.err b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=H3K27ac.err deleted file mode 100644 index 65fb646..0000000 --- a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=H3K27ac.err +++ /dev/null @@ -1,33 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:12:06 2024] -localrule bed_to_gff: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.gff - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/H3K27ac_Optimal_Peaks_bed2gff.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=H3K27ac - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - awk 'BEGIN{OFS=" "} {print $1" ChIPflow peak "$2+1" "$3+1" . . . gene_id "$1"_"$2"_"$3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.gff 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/H3K27ac_Optimal_Peaks_bed2gff.out - - -Activating singularity image epeak.sif -[Thu Sep 12 11:12:07 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=H3K27ac.out b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=H3K27ac.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=Klf4.err b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=Klf4.err deleted file mode 100644 index 556c28e..0000000 --- a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=Klf4.err +++ /dev/null @@ -1,33 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:16:02 2024] -localrule bed_to_gff: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.gff - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/Klf4_Optimal_Peaks_bed2gff.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=Klf4 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - awk 'BEGIN{OFS=" "} {print $1" ChIPflow peak "$2+1" "$3+1" . . . gene_id "$1"_"$2"_"$3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.gff 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/Klf4_Optimal_Peaks_bed2gff.out - - -Activating singularity image epeak.sif -[Thu Sep 12 11:16:03 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=Klf4.out b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=Klf4.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err deleted file mode 100644 index 85a32aa..0000000 --- a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:58:17 2024] -localrule bed_to_gff: - input: RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed - output: RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff - log: RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/logs/ATAC_Optimal_Peaks_bed2gff.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - awk 'BEGIN{OFS=" "} {print $1" ChIPflow peak "$2+1" "$3+1" . . . gene_id "$1"_"$2"_"$3}' RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed > RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff 2> RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/logs/ATAC_Optimal_Peaks_bed2gff.out - - -Activating singularity image epeak.sif -[Thu Sep 12 11:58:17 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.err deleted file mode 100644 index e7a7aec..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7630, disk_mb=13919, disk_mib=13275, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:20:45 2024] -localrule bowtie2_mapping: - input: RES_ATAC/01-Trimming/ATAC_D0_rep1_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D0_rep1_R2_001_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: RES_ATAC/02-Mapping/ATAC_D0_rep1_hg38_sort.bam, RES_ATAC/02-Mapping/ATAC_D0_rep1_hg38.bam - log: RES_ATAC/02-Mapping/logs/ATAC_D0_rep1_hg38_mapping.err, RES_ATAC/02-Mapping/logs/ATAC_D0_rep1_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1, REF=hg38 - resources: mem_mb=47684, mem_mib=7630, disk_mb=13919, disk_mib=13275, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="RES_ATAC/01-Trimming/ATAC_D0_rep1_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D0_rep1_R2_001_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 -X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > RES_ATAC/02-Mapping/ATAC_D0_rep1_hg38.bam" - - # logs - cmd="(${cmd}) > RES_ATAC/02-Mapping/logs/ATAC_D0_rep1_hg38_mapping.out 2> RES_ATAC/02-Mapping/logs/ATAC_D0_rep1_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o RES_ATAC/02-Mapping/ATAC_D0_rep1_hg38_sort.bam RES_ATAC/02-Mapping/ATAC_D0_rep1_hg38.bam " - cmd+=" && samtools index RES_ATAC/02-Mapping/ATAC_D0_rep1_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 18 files and 1 in-memory blocks... -[Thu Sep 12 10:33:30 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.err deleted file mode 100644 index c899ad9..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7630, disk_mb=12370, disk_mib=11797, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:16:43 2024] -localrule bowtie2_mapping: - input: RES_ATAC/01-Trimming/ATAC_D0_rep2_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D0_rep2_R2_001_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: RES_ATAC/02-Mapping/ATAC_D0_rep2_hg38_sort.bam, RES_ATAC/02-Mapping/ATAC_D0_rep2_hg38.bam - log: RES_ATAC/02-Mapping/logs/ATAC_D0_rep2_hg38_mapping.err, RES_ATAC/02-Mapping/logs/ATAC_D0_rep2_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2, REF=hg38 - resources: mem_mb=47684, mem_mib=7630, disk_mb=12370, disk_mib=11797, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="RES_ATAC/01-Trimming/ATAC_D0_rep2_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D0_rep2_R2_001_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 -X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > RES_ATAC/02-Mapping/ATAC_D0_rep2_hg38.bam" - - # logs - cmd="(${cmd}) > RES_ATAC/02-Mapping/logs/ATAC_D0_rep2_hg38_mapping.out 2> RES_ATAC/02-Mapping/logs/ATAC_D0_rep2_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o RES_ATAC/02-Mapping/ATAC_D0_rep2_hg38_sort.bam RES_ATAC/02-Mapping/ATAC_D0_rep2_hg38.bam " - cmd+=" && samtools index RES_ATAC/02-Mapping/ATAC_D0_rep2_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 11 files and 1 in-memory blocks... -[Thu Sep 12 09:41:37 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.err deleted file mode 100644 index 8da4050..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7630, disk_mb=11491, disk_mib=10959, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:13:44 2024] -localrule bowtie2_mapping: - input: RES_ATAC/01-Trimming/ATAC_D0_rep3_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D0_rep3_R2_001_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: RES_ATAC/02-Mapping/ATAC_D0_rep3_hg38_sort.bam, RES_ATAC/02-Mapping/ATAC_D0_rep3_hg38.bam - log: RES_ATAC/02-Mapping/logs/ATAC_D0_rep3_hg38_mapping.err, RES_ATAC/02-Mapping/logs/ATAC_D0_rep3_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3, REF=hg38 - resources: mem_mb=47684, mem_mib=7630, disk_mb=11491, disk_mib=10959, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="RES_ATAC/01-Trimming/ATAC_D0_rep3_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D0_rep3_R2_001_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 -X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > RES_ATAC/02-Mapping/ATAC_D0_rep3_hg38.bam" - - # logs - cmd="(${cmd}) > RES_ATAC/02-Mapping/logs/ATAC_D0_rep3_hg38_mapping.out 2> RES_ATAC/02-Mapping/logs/ATAC_D0_rep3_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o RES_ATAC/02-Mapping/ATAC_D0_rep3_hg38_sort.bam RES_ATAC/02-Mapping/ATAC_D0_rep3_hg38.bam " - cmd+=" && samtools index RES_ATAC/02-Mapping/ATAC_D0_rep3_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 7 files and 1 in-memory blocks... -[Thu Sep 12 07:05:07 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.err deleted file mode 100644 index 037c994..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6884, disk_mb=7218, disk_mib=6884, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:59:39 2024] -localrule bowtie2_mapping: - input: RES_ATAC/01-Trimming/ATAC_D6F_rep1_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6F_rep1_R2_001_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: RES_ATAC/02-Mapping/ATAC_D6F_rep1_hg38_sort.bam, RES_ATAC/02-Mapping/ATAC_D6F_rep1_hg38.bam - log: RES_ATAC/02-Mapping/logs/ATAC_D6F_rep1_hg38_mapping.err, RES_ATAC/02-Mapping/logs/ATAC_D6F_rep1_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1, REF=hg38 - resources: mem_mb=47684, mem_mib=6884, disk_mb=7218, disk_mib=6884, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="RES_ATAC/01-Trimming/ATAC_D6F_rep1_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6F_rep1_R2_001_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 -X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > RES_ATAC/02-Mapping/ATAC_D6F_rep1_hg38.bam" - - # logs - cmd="(${cmd}) > RES_ATAC/02-Mapping/logs/ATAC_D6F_rep1_hg38_mapping.out 2> RES_ATAC/02-Mapping/logs/ATAC_D6F_rep1_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o RES_ATAC/02-Mapping/ATAC_D6F_rep1_hg38_sort.bam RES_ATAC/02-Mapping/ATAC_D6F_rep1_hg38.bam " - cmd+=" && samtools index RES_ATAC/02-Mapping/ATAC_D6F_rep1_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 21 files and 1 in-memory blocks... -[Thu Sep 12 00:28:48 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.err deleted file mode 100644 index 46b0a6a..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6897, disk_mb=7231, disk_mib=6897, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:00:38 2024] -localrule bowtie2_mapping: - input: RES_ATAC/01-Trimming/ATAC_D6F_rep2_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6F_rep2_R2_001_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: RES_ATAC/02-Mapping/ATAC_D6F_rep2_hg38_sort.bam, RES_ATAC/02-Mapping/ATAC_D6F_rep2_hg38.bam - log: RES_ATAC/02-Mapping/logs/ATAC_D6F_rep2_hg38_mapping.err, RES_ATAC/02-Mapping/logs/ATAC_D6F_rep2_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2, REF=hg38 - resources: mem_mb=47684, mem_mib=6897, disk_mb=7231, disk_mib=6897, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="RES_ATAC/01-Trimming/ATAC_D6F_rep2_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6F_rep2_R2_001_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 -X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > RES_ATAC/02-Mapping/ATAC_D6F_rep2_hg38.bam" - - # logs - cmd="(${cmd}) > RES_ATAC/02-Mapping/logs/ATAC_D6F_rep2_hg38_mapping.out 2> RES_ATAC/02-Mapping/logs/ATAC_D6F_rep2_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o RES_ATAC/02-Mapping/ATAC_D6F_rep2_hg38_sort.bam RES_ATAC/02-Mapping/ATAC_D6F_rep2_hg38.bam " - cmd+=" && samtools index RES_ATAC/02-Mapping/ATAC_D6F_rep2_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 21 files and 1 in-memory blocks... -[Wed Sep 11 23:30:35 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.err deleted file mode 100644 index 0203907..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7630, disk_mb=8369, disk_mib=7982, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:02:37 2024] -localrule bowtie2_mapping: - input: RES_ATAC/01-Trimming/ATAC_D6F_rep3_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6F_rep3_R2_001_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: RES_ATAC/02-Mapping/ATAC_D6F_rep3_hg38_sort.bam, RES_ATAC/02-Mapping/ATAC_D6F_rep3_hg38.bam - log: RES_ATAC/02-Mapping/logs/ATAC_D6F_rep3_hg38_mapping.err, RES_ATAC/02-Mapping/logs/ATAC_D6F_rep3_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3, REF=hg38 - resources: mem_mb=47684, mem_mib=7630, disk_mb=8369, disk_mib=7982, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="RES_ATAC/01-Trimming/ATAC_D6F_rep3_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6F_rep3_R2_001_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 -X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > RES_ATAC/02-Mapping/ATAC_D6F_rep3_hg38.bam" - - # logs - cmd="(${cmd}) > RES_ATAC/02-Mapping/logs/ATAC_D6F_rep3_hg38_mapping.out 2> RES_ATAC/02-Mapping/logs/ATAC_D6F_rep3_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o RES_ATAC/02-Mapping/ATAC_D6F_rep3_hg38_sort.bam RES_ATAC/02-Mapping/ATAC_D6F_rep3_hg38.bam " - cmd+=" && samtools index RES_ATAC/02-Mapping/ATAC_D6F_rep3_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 26 files and 1 in-memory blocks... -[Thu Sep 12 01:42:57 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.err deleted file mode 100644 index ed0f7a4..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7275, disk_mb=7628, disk_mib=7275, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:00:37 2024] -localrule bowtie2_mapping: - input: RES_ATAC/01-Trimming/ATAC_D6_rep1_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6_rep1_R2_001_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: RES_ATAC/02-Mapping/ATAC_D6_rep1_hg38_sort.bam, RES_ATAC/02-Mapping/ATAC_D6_rep1_hg38.bam - log: RES_ATAC/02-Mapping/logs/ATAC_D6_rep1_hg38_mapping.err, RES_ATAC/02-Mapping/logs/ATAC_D6_rep1_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1, REF=hg38 - resources: mem_mb=47684, mem_mib=7275, disk_mb=7628, disk_mib=7275, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="RES_ATAC/01-Trimming/ATAC_D6_rep1_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6_rep1_R2_001_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 -X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > RES_ATAC/02-Mapping/ATAC_D6_rep1_hg38.bam" - - # logs - cmd="(${cmd}) > RES_ATAC/02-Mapping/logs/ATAC_D6_rep1_hg38_mapping.out 2> RES_ATAC/02-Mapping/logs/ATAC_D6_rep1_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o RES_ATAC/02-Mapping/ATAC_D6_rep1_hg38_sort.bam RES_ATAC/02-Mapping/ATAC_D6_rep1_hg38.bam " - cmd+=" && samtools index RES_ATAC/02-Mapping/ATAC_D6_rep1_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 23 files and 1 in-memory blocks... -[Wed Sep 11 23:59:10 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.err deleted file mode 100644 index a050933..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7630, disk_mb=9561, disk_mib=9119, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:06:45 2024] -localrule bowtie2_mapping: - input: RES_ATAC/01-Trimming/ATAC_D6_rep2_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6_rep2_R2_001_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: RES_ATAC/02-Mapping/ATAC_D6_rep2_hg38_sort.bam, RES_ATAC/02-Mapping/ATAC_D6_rep2_hg38.bam - log: RES_ATAC/02-Mapping/logs/ATAC_D6_rep2_hg38_mapping.err, RES_ATAC/02-Mapping/logs/ATAC_D6_rep2_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2, REF=hg38 - resources: mem_mb=47684, mem_mib=7630, disk_mb=9561, disk_mib=9119, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="RES_ATAC/01-Trimming/ATAC_D6_rep2_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6_rep2_R2_001_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 -X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > RES_ATAC/02-Mapping/ATAC_D6_rep2_hg38.bam" - - # logs - cmd="(${cmd}) > RES_ATAC/02-Mapping/logs/ATAC_D6_rep2_hg38_mapping.out 2> RES_ATAC/02-Mapping/logs/ATAC_D6_rep2_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o RES_ATAC/02-Mapping/ATAC_D6_rep2_hg38_sort.bam RES_ATAC/02-Mapping/ATAC_D6_rep2_hg38.bam " - cmd+=" && samtools index RES_ATAC/02-Mapping/ATAC_D6_rep2_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 31 files and 1 in-memory blocks... -[Thu Sep 12 04:41:55 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.err deleted file mode 100644 index 014fb2e..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7630, disk_mb=12015, disk_mib=11459, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:14:43 2024] -localrule bowtie2_mapping: - input: RES_ATAC/01-Trimming/ATAC_D6_rep3_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6_rep3_R2_001_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: RES_ATAC/02-Mapping/ATAC_D6_rep3_hg38_sort.bam, RES_ATAC/02-Mapping/ATAC_D6_rep3_hg38.bam - log: RES_ATAC/02-Mapping/logs/ATAC_D6_rep3_hg38_mapping.err, RES_ATAC/02-Mapping/logs/ATAC_D6_rep3_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3, REF=hg38 - resources: mem_mb=47684, mem_mib=7630, disk_mb=12015, disk_mib=11459, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="RES_ATAC/01-Trimming/ATAC_D6_rep3_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6_rep3_R2_001_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 -X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > RES_ATAC/02-Mapping/ATAC_D6_rep3_hg38.bam" - - # logs - cmd="(${cmd}) > RES_ATAC/02-Mapping/logs/ATAC_D6_rep3_hg38_mapping.out 2> RES_ATAC/02-Mapping/logs/ATAC_D6_rep3_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o RES_ATAC/02-Mapping/ATAC_D6_rep3_hg38_sort.bam RES_ATAC/02-Mapping/ATAC_D6_rep3_hg38.bam " - cmd+=" && samtools index RES_ATAC/02-Mapping/ATAC_D6_rep3_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 10 files and 1 in-memory blocks... -[Thu Sep 12 09:46:34 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index a37d987..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6629, disk_mb=6951, disk_mib=6629, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:12:01 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep1_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep1_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=hg38 - resources: mem_mb=47684, mem_mib=6629, disk_mb=6951, disk_mib=6629, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep1_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep1_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 18 files and 1 in-memory blocks... -[Tue Aug 27 14:30:14 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 8934a25..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6460, disk_mb=6773, disk_mib=6460, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:19:10 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep1_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep1_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=mm10 - resources: mem_mb=47684, mem_mib=6460, disk_mb=6773, disk_mib=6460, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep1_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep1_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 22 files and 1 in-memory blocks... -[Wed Sep 11 21:04:12 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index 6370f5c..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6896, disk_mb=7230, disk_mib=6896, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:12:52 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep2_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep2_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=hg38 - resources: mem_mb=47684, mem_mib=6896, disk_mb=7230, disk_mib=6896, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep2_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep2_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 19 files and 1 in-memory blocks... -[Tue Aug 27 14:31:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index ffa9d68..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6725, disk_mb=7051, disk_mib=6725, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:20:11 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep2_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep2_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=mm10 - resources: mem_mb=47684, mem_mib=6725, disk_mb=7051, disk_mib=6725, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep2_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shCtrl_Rep2_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 23 files and 1 in-memory blocks... -[Wed Sep 11 22:03:11 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index 87deb99..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7570, disk_mb=7937, disk_mib=7570, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:15:55 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep1_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep1_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=hg38 - resources: mem_mb=47684, mem_mib=7570, disk_mb=7937, disk_mib=7570, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep1_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep1_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 22 files and 1 in-memory blocks... -[Tue Aug 27 15:01:40 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 9e5d46b..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7400, disk_mb=7759, disk_mib=7400, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:23:02 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep1_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep1_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=mm10 - resources: mem_mb=47684, mem_mib=7400, disk_mb=7759, disk_mib=7400, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep1_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep1_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 26 files and 1 in-memory blocks... -[Wed Sep 11 21:30:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index 6874e62..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6287, disk_mb=6592, disk_mib=6287, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:09:58 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep2_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep2_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=hg38 - resources: mem_mb=47684, mem_mib=6287, disk_mb=6592, disk_mib=6287, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep2_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep2_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 17 files and 1 in-memory blocks... -[Tue Aug 27 14:38:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 9c2bc1e..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6116, disk_mb=6413, disk_mib=6116, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:16:07 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep2_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep2_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=mm10 - resources: mem_mb=47684, mem_mib=6116, disk_mb=6413, disk_mib=6116, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep2_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/H3K27ac_shUbc9_Rep2_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 20 files and 1 in-memory blocks... -[Wed Sep 11 20:40:03 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index ecfc91d..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=5996, disk_mb=6287, disk_mib=5996, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:10:01 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep1_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep1_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=hg38 - resources: mem_mb=47684, mem_mib=5996, disk_mb=6287, disk_mib=5996, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep1_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep1_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 18 files and 1 in-memory blocks... -[Tue Aug 27 14:52:30 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 34e7e88..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=5826, disk_mb=6109, disk_mib=5826, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:17:06 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep1_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep1_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=mm10 - resources: mem_mb=47684, mem_mib=5826, disk_mb=6109, disk_mib=5826, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep1_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep1_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 21 files and 1 in-memory blocks... -[Wed Sep 11 22:50:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index 7de24c5..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6588, disk_mb=6907, disk_mib=6588, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:13:52 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep2_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep2_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=hg38 - resources: mem_mb=47684, mem_mib=6588, disk_mb=6907, disk_mib=6588, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep2_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep2_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 20 files and 1 in-memory blocks... -[Tue Aug 27 15:10:36 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index cdbfbec..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6418, disk_mb=6729, disk_mib=6418, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:20:11 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep2_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep2_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=mm10 - resources: mem_mb=47684, mem_mib=6418, disk_mb=6729, disk_mib=6418, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep2_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shCtrl_Rep2_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 24 files and 1 in-memory blocks... -[Thu Sep 12 01:14:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index 93f316d..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6592, disk_mb=6912, disk_mib=6592, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:13:52 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep1_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep1_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=hg38 - resources: mem_mb=47684, mem_mib=6592, disk_mb=6912, disk_mib=6592, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep1_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep1_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 21 files and 1 in-memory blocks... -[Tue Aug 27 15:18:35 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 789a431..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6423, disk_mb=6734, disk_mib=6423, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:21:13 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep1_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep1_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=mm10 - resources: mem_mb=47684, mem_mib=6423, disk_mb=6734, disk_mib=6423, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep1_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep1_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 25 files and 1 in-memory blocks... -[Wed Sep 11 23:25:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index d09dbc1..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6929, disk_mb=7265, disk_mib=6929, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:15:55 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep2_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep2_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=hg38 - resources: mem_mb=47684, mem_mib=6929, disk_mb=7265, disk_mib=6929, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep2_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep2_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 22 files and 1 in-memory blocks... -[Tue Aug 27 15:45:35 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 1ba52f2..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6759, disk_mb=7087, disk_mib=6759, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:23:06 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep2_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep2_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=mm10 - resources: mem_mb=47684, mem_mib=6759, disk_mb=7087, disk_mib=6759, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep2_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/INPUT_shUbc9_Rep2_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 26 files and 1 in-memory blocks... -[Wed Sep 11 23:41:20 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index ff937bd..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=5929, disk_mb=6216, disk_mib=5929, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:11:02 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep1_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep1_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=hg38 - resources: mem_mb=47684, mem_mib=5929, disk_mb=6216, disk_mib=5929, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep1_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep1_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 18 files and 1 in-memory blocks... -[Tue Aug 27 14:24:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 3e0c3c0..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=5759, disk_mb=6038, disk_mib=5759, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:17:06 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep1_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep1_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=mm10 - resources: mem_mb=47684, mem_mib=5759, disk_mb=6038, disk_mib=5759, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep1_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep1_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 21 files and 1 in-memory blocks... -[Wed Sep 11 21:10:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index 339905d..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=5565, disk_mb=5835, disk_mib=5565, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:08:00 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep2_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep2_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=hg38 - resources: mem_mb=47684, mem_mib=5565, disk_mb=5835, disk_mib=5565, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep2_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep2_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 16 files and 1 in-memory blocks... -[Tue Aug 27 14:31:21 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index d5795f9..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=5395, disk_mb=5657, disk_mib=5395, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:15:06 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep2_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep2_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=mm10 - resources: mem_mb=47684, mem_mib=5395, disk_mb=5657, disk_mib=5395, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep2_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shCtrl_Rep2_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 19 files and 1 in-memory blocks... -[Wed Sep 11 20:36:03 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index b2f467c..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6058, disk_mb=6352, disk_mib=6058, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:11:02 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep1_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep1_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=hg38 - resources: mem_mb=47684, mem_mib=6058, disk_mb=6352, disk_mib=6058, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep1_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep1_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 18 files and 1 in-memory blocks... -[Tue Aug 27 14:48:07 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 33d93c7..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=5888, disk_mb=6174, disk_mib=5888, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:17:06 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep1_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep1_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep1_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=mm10 - resources: mem_mb=47684, mem_mib=5888, disk_mb=6174, disk_mib=5888, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep1_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep1_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep1_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 22 files and 1 in-memory blocks... -[Wed Sep 11 22:26:33 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index ad47acd..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6969, disk_mb=7307, disk_mib=6969, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 12:15:55 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_hg38_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_hg38.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep2_hg38_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep2_hg38_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=hg38 - resources: mem_mb=47684, mem_mib=6969, disk_mb=7307, disk_mib=6969, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_hg38.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep2_hg38_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep2_hg38_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_hg38_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_hg38.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_hg38_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 22 files and 1 in-memory blocks... -[Tue Aug 27 15:11:29 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 27dbdaf..0000000 --- a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,58 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6799, disk_mb=7129, disk_mib=6799, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 16:24:07 2024] -localrule bowtie2_mapping: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep2_R1_trim.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10.1.bt2 - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_mm10_sort.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_mm10.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep2_mm10_mapping.err, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep2_mm10_mapping.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=mm10 - resources: mem_mb=47684, mem_mib=6799, disk_mb=7129, disk_mib=6799, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep2_R1_trim.fastq.gz" - infiles=($tmp) - - cmd="bowtie2 -p 1 --very-sensitive -x /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]] - then - bowtie_input=" -1 ${infiles[0]} -2 ${infiles[1]} " - else - bowtie_input=" -U ${infiles[0]} " - fi - - cmd+=" ${bowtie_input}" - # sam to bam - cmd+=" | samtools view -Sbh - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_mm10.bam" - - # logs - cmd="(${cmd}) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep2_mm10_mapping.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/logs/Klf4_shUbc9_Rep2_mm10_mapping.err" - - # sort result - cmd+=" && samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_mm10_sort.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_mm10.bam " - cmd+=" && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_mm10_sort.bam" - - #run command - eval "${cmd}" - -Activating singularity image epeak.sif -[bam_sort_core] merging from 26 files and 1 in-memory blocks... -[Wed Sep 11 22:20:07 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.err b/logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index 49bf0d3..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,45 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:43:06 2024] -localrule chipflowr: - input: RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale/config.R - output: RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale/ATAC_Stat_report_Limma_scale.html - log: RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale/ATAC_Limma_scale_Log.txt - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - set +u - # change directory - cwd=`pwd` - # copy Rmd and needed files - cp ${cwd}/workflow/scripts/Report_ChIPflowR.Rmd RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale - cp ${cwd}/workflow/scripts/bibliography.bib RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale - cp ${cwd}/workflow/scripts/medecine-sciences.csl RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale - cd RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale - # load the Rmarkdown - outfile=$(basename RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale/ATAC_Stat_report_Limma_scale.html) - logs=$(basename RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale/ATAC_Limma_scale_Log.txt) - Rscript -e "rmarkdown::render(input='Report_ChIPflowR.Rmd', output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" 2> ${logs} - #Rscript -e "rmarkdown::render(input=system.file('Report_ChIPflowR.Rmd', package='ChIPflowR'), output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" - cd $cwd - - -Activating singularity image epeak.sif -[Thu Sep 12 12:43:44 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.out b/logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index 499c5fb..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.out +++ /dev/null @@ -1,38 +0,0 @@ -1/37 -2/37 [unnamed-chunk-1] -3/37 -4/37 [unnamed-chunk-2] -5/37 -6/37 [unnamed-chunk-3] -7/37 -8/37 [unnamed-chunk-4] -9/37 -10/37 [unnamed-chunk-5] -11/37 -12/37 [barplot] -13/37 -14/37 [pairewiseScatter] -15/37 -16/37 [clusterplot] -17/37 -18/37 [PCA] -19/37 -20/37 [unnamed-chunk-6] -21/37 -22/37 [unnamed-chunk-7] -23/37 -24/37 [boxplot] -25/37 -26/37 [dispersionPlot] -27/37 -28/37 [meanvar] -29/37 -30/37 [unnamed-chunk-8] -31/37 -32/37 [unnamed-chunk-9] -33/37 -34/37 [MAplot] -35/37 -36/37 [unnamed-chunk-10] -37/37 -/usr/bin/pandoc +RTS -K512m -RTS Report_ChIPflowR.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output ATAC_Stat_report_Limma_scale.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 2 --variable toc_float=1 --variable toc_selectors=h1,h2 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /pasteur/appa/scratch/rlegendr/RtmphL0Ufd/rmarkdown-str3d51b95e8ee5c3.html --filter /usr/bin/pandoc-citeproc diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err b/logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index 0a87d0f..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,45 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 13:14:00 2024] -localrule chipflowr: - input: RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale/config.R - output: RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale/ATAC_Stat_report_Limma_scale.html - log: RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale/ATAC_Limma_scale_Log.txt - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - set +u - # change directory - cwd=`pwd` - # copy Rmd and needed files - cp ${cwd}/workflow/scripts/Report_ChIPflowR.Rmd RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale - cp ${cwd}/workflow/scripts/bibliography.bib RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale - cp ${cwd}/workflow/scripts/medecine-sciences.csl RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale - cd RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale - # load the Rmarkdown - outfile=$(basename RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale/ATAC_Stat_report_Limma_scale.html) - logs=$(basename RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale/ATAC_Limma_scale_Log.txt) - Rscript -e "rmarkdown::render(input='Report_ChIPflowR.Rmd', output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" 2> ${logs} - #Rscript -e "rmarkdown::render(input=system.file('Report_ChIPflowR.Rmd', package='ChIPflowR'), output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" - cd $cwd - - -Activating singularity image epeak.sif -[Thu Sep 12 13:14:40 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out b/logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index ae9ce67..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out +++ /dev/null @@ -1,38 +0,0 @@ -1/37 -2/37 [unnamed-chunk-1] -3/37 -4/37 [unnamed-chunk-2] -5/37 -6/37 [unnamed-chunk-3] -7/37 -8/37 [unnamed-chunk-4] -9/37 -10/37 [unnamed-chunk-5] -11/37 -12/37 [barplot] -13/37 -14/37 [pairewiseScatter] -15/37 -16/37 [clusterplot] -17/37 -18/37 [PCA] -19/37 -20/37 [unnamed-chunk-6] -21/37 -22/37 [unnamed-chunk-7] -23/37 -24/37 [boxplot] -25/37 -26/37 [dispersionPlot] -27/37 -28/37 [meanvar] -29/37 -30/37 [unnamed-chunk-8] -31/37 -32/37 [unnamed-chunk-9] -33/37 -34/37 [MAplot] -35/37 -36/37 [unnamed-chunk-10] -37/37 -/usr/bin/pandoc +RTS -K512m -RTS Report_ChIPflowR.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output ATAC_Stat_report_Limma_scale.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 2 --variable toc_float=1 --variable toc_selectors=h1,h2 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /pasteur/appa/scratch/rlegendr/RtmpAjMydh/rmarkdown-str9e49471913263.html --filter /usr/bin/pandoc-citeproc diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.err b/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.err deleted file mode 100644 index c6d01f9..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.err +++ /dev/null @@ -1,75 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:16:49 2024] -localrule chipflowr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/config.R - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Limma_scale_Log.txt - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=H3K27ac - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - set +u - # change directory - cwd=`pwd` - # copy Rmd and needed files - cp ${cwd}/workflow/scripts/Report_ChIPflowR.Rmd /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale - cp ${cwd}/workflow/scripts/bibliography.bib /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale - cp ${cwd}/workflow/scripts/medecine-sciences.csl /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale - cd /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale - # load the Rmarkdown - outfile=$(basename /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html) - logs=$(basename /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Limma_scale_Log.txt) - Rscript -e "rmarkdown::render(input='Report_ChIPflowR.Rmd', output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" 2> ${logs} - #Rscript -e "rmarkdown::render(input=system.file('Report_ChIPflowR.Rmd', package='ChIPflowR'), output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" - cd $cwd - - -Activating singularity image epeak.sif -[Thu Sep 12 11:17:08 2024] -Error in rule chipflowr: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/config.R - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Limma_scale_Log.txt (check log file(s) for error details) - shell: - - set +o pipefail - set +u - # change directory - cwd=`pwd` - # copy Rmd and needed files - cp ${cwd}/workflow/scripts/Report_ChIPflowR.Rmd /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale - cp ${cwd}/workflow/scripts/bibliography.bib /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale - cp ${cwd}/workflow/scripts/medecine-sciences.csl /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale - cd /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale - # load the Rmarkdown - outfile=$(basename /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html) - logs=$(basename /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Limma_scale_Log.txt) - Rscript -e "rmarkdown::render(input='Report_ChIPflowR.Rmd', output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" 2> ${logs} - #Rscript -e "rmarkdown::render(input=system.file('Report_ChIPflowR.Rmd', package='ChIPflowR'), output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" - cd $cwd - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.out b/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.out deleted file mode 100644 index f2f0e3c..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.out +++ /dev/null @@ -1,4 +0,0 @@ -1/37 -2/37 [unnamed-chunk-1] -3/37 -4/37 [unnamed-chunk-2] diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.err b/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.err deleted file mode 100644 index da4e248..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 19:38:51 2024] -localrule chipflowr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/config.R - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Stat_report_Limma_scale.html - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Limma_scale_Log.txt - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=Klf4 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - set +u - # change directory - cwd=`pwd` - # copy Rmd and needed files - cp ${cwd}/workflow/scripts/Report_ChIPflowR.Rmd /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale - cp ${cwd}/workflow/scripts/bibliography.bib /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale - cp ${cwd}/workflow/scripts/medecine-sciences.csl /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale - cd /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale - # load the Rmarkdown - outfile=$(basename /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Stat_report_Limma_scale.html) - logs=$(basename /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Limma_scale_Log.txt) - Rscript -e "rmarkdown::render(input='Report_ChIPflowR.Rmd', output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" 2> ${logs} - #Rscript -e "rmarkdown::render(input=system.file('Report_ChIPflowR.Rmd', package='ChIPflowR'), output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" - cd $cwd - - -Activating singularity image epeak.sif -[Thu Sep 5 19:39:23 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.out b/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.out deleted file mode 100644 index 36d347b..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.out +++ /dev/null @@ -1,38 +0,0 @@ -1/37 -2/37 [unnamed-chunk-1] -3/37 -4/37 [unnamed-chunk-2] -5/37 -6/37 [unnamed-chunk-3] -7/37 -8/37 [unnamed-chunk-4] -9/37 -10/37 [unnamed-chunk-5] -11/37 -12/37 [barplot] -13/37 -14/37 [pairewiseScatter] -15/37 -16/37 [clusterplot] -17/37 -18/37 [PCA] -19/37 -20/37 [unnamed-chunk-6] -21/37 -22/37 [unnamed-chunk-7] -23/37 -24/37 [boxplot] -25/37 -26/37 [dispersionPlot] -27/37 -28/37 [meanvar] -29/37 -30/37 [unnamed-chunk-8] -31/37 -32/37 [unnamed-chunk-9] -33/37 -34/37 [MAplot] -35/37 -36/37 [unnamed-chunk-10] -37/37 -/usr/bin/pandoc +RTS -K512m -RTS Report_ChIPflowR.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Klf4_Stat_report_Limma_scale.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 2 --variable toc_float=1 --variable toc_selectors=h1,h2 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /pasteur/appa/scratch/rlegendr/Rtmphgu6Bh/rmarkdown-strdeb0a20282e30.html --filter /usr/bin/pandoc-citeproc diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err b/logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err deleted file mode 100644 index 6865148..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err +++ /dev/null @@ -1,45 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:14:02 2024] -localrule chipflowr: - input: RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale/config.R - output: RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale/ATAC_Stat_report_Limma_scale.html - log: RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale/ATAC_Limma_scale_Log.txt - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - set +u - # change directory - cwd=`pwd` - # copy Rmd and needed files - cp ${cwd}/workflow/scripts/Report_ChIPflowR.Rmd RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale - cp ${cwd}/workflow/scripts/bibliography.bib RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale - cp ${cwd}/workflow/scripts/medecine-sciences.csl RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale - cd RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale - # load the Rmarkdown - outfile=$(basename RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale/ATAC_Stat_report_Limma_scale.html) - logs=$(basename RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale/ATAC_Limma_scale_Log.txt) - Rscript -e "rmarkdown::render(input='Report_ChIPflowR.Rmd', output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" 2> ${logs} - #Rscript -e "rmarkdown::render(input=system.file('Report_ChIPflowR.Rmd', package='ChIPflowR'), output_file='${outfile}', run_pandoc=TRUE, clean=TRUE)" - cd $cwd - - -Activating singularity image epeak.sif -[Thu Sep 12 12:14:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out b/logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out deleted file mode 100644 index fbdbf44..0000000 --- a/logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out +++ /dev/null @@ -1,38 +0,0 @@ -1/37 -2/37 [unnamed-chunk-1] -3/37 -4/37 [unnamed-chunk-2] -5/37 -6/37 [unnamed-chunk-3] -7/37 -8/37 [unnamed-chunk-4] -9/37 -10/37 [unnamed-chunk-5] -11/37 -12/37 [barplot] -13/37 -14/37 [pairewiseScatter] -15/37 -16/37 [clusterplot] -17/37 -18/37 [PCA] -19/37 -20/37 [unnamed-chunk-6] -21/37 -22/37 [unnamed-chunk-7] -23/37 -24/37 [boxplot] -25/37 -26/37 [dispersionPlot] -27/37 -28/37 [meanvar] -29/37 -30/37 [unnamed-chunk-8] -31/37 -32/37 [unnamed-chunk-9] -33/37 -34/37 [MAplot] -35/37 -36/37 [unnamed-chunk-10] -37/37 -/usr/bin/pandoc +RTS -K512m -RTS Report_ChIPflowR.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output ATAC_Stat_report_Limma_scale.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 2 --variable toc_float=1 --variable toc_selectors=h1,h2 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /pasteur/appa/scratch/rlegendr/RtmpHqbyGQ/rmarkdown-str302ca85f7b597b.html --filter /usr/bin/pandoc-citeproc diff --git a/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=H3K27ac.err b/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=H3K27ac.err deleted file mode 100644 index 3a595a5..0000000 --- a/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=H3K27ac.err +++ /dev/null @@ -1,63 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:22 2024] -localrule chipflowr_annotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.log - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=H3K27ac - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_analysis_diff.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt `dirname /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html` >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.log 2>&1 - else - sh workflow/scripts/annote_analysis_diff.sh config/annotation_config.txt `dirname /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html` >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.log 2>&1 - fi - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.done - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:47 2024] -Error in rule chipflowr_annotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.log (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_analysis_diff.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt `dirname /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html` >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.log 2>&1 - else - sh workflow/scripts/annote_analysis_diff.sh config/annotation_config.txt `dirname /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/H3K27ac_Stat_report_Limma_scale.html` >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.log 2>&1 - fi - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results/annotation.done - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Removing output files of failed job chipflowr_annotation since they might be corrupted: -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/annotated_results -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=H3K27ac.out b/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=H3K27ac.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=Klf4.err b/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=Klf4.err deleted file mode 100644 index a17840c..0000000 --- a/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=Klf4.err +++ /dev/null @@ -1,63 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:22 2024] -localrule chipflowr_annotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Stat_report_Limma_scale.html - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.log - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=Klf4 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_analysis_diff.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt `dirname /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Stat_report_Limma_scale.html` >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.log 2>&1 - else - sh workflow/scripts/annote_analysis_diff.sh config/annotation_config.txt `dirname /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Stat_report_Limma_scale.html` >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.log 2>&1 - fi - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.done - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:47 2024] -Error in rule chipflowr_annotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Stat_report_Limma_scale.html - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.log (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_analysis_diff.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt `dirname /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Stat_report_Limma_scale.html` >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.log 2>&1 - else - sh workflow/scripts/annote_analysis_diff.sh config/annotation_config.txt `dirname /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/Klf4_Stat_report_Limma_scale.html` >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.log 2>&1 - fi - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results/annotation.done - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Removing output files of failed job chipflowr_annotation since they might be corrupted: -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/annotated_results -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=Klf4.out b/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=Klf4.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=genrich.MOD=narrow.MARK=ATAC.err b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=genrich.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index 25f003f..0000000 --- a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=genrich.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,26 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:42:54 2024] -localrule chipflowr_init: - input: RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_Matrix_Optimal_Peak.mtx, RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_Matrix_Optimal_Peak.mtx - output: RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale/config.R - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -sed -i -E 's/((\/?[A-Za-z0-9._-]+){0,})(\/04-NobiasedRegions\/)//g' RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_Matrix_Optimal_Peak.mtx && sed -i 's/_hg38_sort_dedup_biasedRegions.bam//g' RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_Matrix_Optimal_Peak.mtx -[Thu Sep 12 12:42:54 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=genrich.MOD=narrow.MARK=ATAC.out b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=genrich.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index b5f0924..0000000 --- a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,26 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 13:13:46 2024] -localrule chipflowr_init: - input: RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_Matrix_Optimal_Peak.mtx, RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_Matrix_Optimal_Peak.mtx - output: RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale/config.R - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -sed -i -E 's/((\/?[A-Za-z0-9._-]+){0,})(\/04-NobiasedRegions\/)//g' RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_Matrix_Optimal_Peak.mtx && sed -i 's/_hg38_sort_dedup_biasedRegions.bam//g' RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_Matrix_Optimal_Peak.mtx -[Thu Sep 12 13:13:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=H3K27ac.err b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=H3K27ac.err deleted file mode 100644 index c2a8383..0000000 --- a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=H3K27ac.err +++ /dev/null @@ -1,28 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:15:47 2024] -localrule chipflowr_init: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_Matrix_Optimal_Peak.mtx, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_Matrix_Optimal_Peak.mtx - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/10-DifferentialAnalysis/macs2_narrow/H3K27ac_Limma_scale/config.R - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=H3K27ac - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -sed -i -E 's/((\/?[A-Za-z0-9._-]+){0,})(\/04-NobiasedRegions\/)//g' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_Matrix_Optimal_Peak.mtx && sed -i 's/_mm10_sort_dedup_biasedRegions.bam//g' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_Matrix_Optimal_Peak.mtx -[Thu Sep 12 11:15:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=H3K27ac.out b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=H3K27ac.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=Klf4.err b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=Klf4.err deleted file mode 100644 index cfb00a3..0000000 --- a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=Klf4.err +++ /dev/null @@ -1,28 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 19:38:38 2024] -localrule chipflowr_init: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/09-CountMatrix/macs2_narrow/Klf4_Matrix_Optimal_Peak.mtx, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/09-CountMatrix/macs2_narrow/Klf4_Matrix_Optimal_Peak.mtx - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/10-DifferentialAnalysis/macs2_narrow/Klf4_Limma_scale/config.R - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=Klf4 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -sed -i -E 's/((\/[A-Za-z0-9._-]+){0,})(\/04-NobiasedRegions\/)//g' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/09-CountMatrix/macs2_narrow/Klf4_Matrix_Optimal_Peak.mtx && sed -i 's/_mm10_sort_dedup_biasedRegions.bam//g' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/09-CountMatrix/macs2_narrow/Klf4_Matrix_Optimal_Peak.mtx -[Thu Sep 5 19:38:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=Klf4.out b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=Klf4.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err deleted file mode 100644 index b14935a..0000000 --- a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err +++ /dev/null @@ -1,26 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:13:50 2024] -localrule chipflowr_init: - input: RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_Matrix_Optimal_Peak.mtx, RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_Matrix_Optimal_Peak.mtx - output: RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale/config.R - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -sed -i -E 's/((\/?[A-Za-z0-9._-]+){0,})(\/04-NobiasedRegions\/)//g' RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_Matrix_Optimal_Peak.mtx && sed -i 's/_hg38_sort_dedup_biasedRegions.bam//g' RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_Matrix_Optimal_Peak.mtx -[Thu Sep 12 12:13:51 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err b/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err deleted file mode 100644 index b3df6d2..0000000 --- a/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:16:02 2024] -localrule chipr: - input: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_log.txt - log: RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D0_log.out, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D0_log.err - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, FORM=narrow, IP_NAME=ATAC_D0 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak -m 2 --rankmethod signalvalue -o RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE > RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D0_log.out 2> RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D0_log.err - - -Activating singularity image epeak.sif -[Thu Sep 12 12:26:00 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.out b/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err b/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err deleted file mode 100644 index 996d221..0000000 --- a/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:15:59 2024] -localrule chipr: - input: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_log.txt - log: RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D6_log.out, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D6_log.err - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, FORM=narrow, IP_NAME=ATAC_D6 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak -m 2 --rankmethod signalvalue -o RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE > RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D6_log.out 2> RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D6_log.err - - -Activating singularity image epeak.sif -[Thu Sep 12 12:26:08 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.out b/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err b/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err deleted file mode 100644 index 87aedbc..0000000 --- a/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:15:53 2024] -localrule chipr: - input: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_log.txt - log: RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D6F_log.out, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D6F_log.err - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, FORM=narrow, IP_NAME=ATAC_D6F - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak -m 2 --rankmethod signalvalue -o RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE > RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D6F_log.out 2> RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/logs/ATAC_D6F_log.err - - -Activating singularity image epeak.sif -[Thu Sep 12 12:25:23 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.out b/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err b/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err deleted file mode 100644 index 5c68c87..0000000 --- a/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:11:18 2024] -localrule chipr: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_log.txt - log: RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D0_log.out, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D0_log.err - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, FORM=narrow, IP_NAME=ATAC_D0 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak -m 2 --rankmethod signalvalue -o RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE > RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D0_log.out 2> RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D0_log.err - - -Activating singularity image epeak.sif -[Thu Sep 12 12:58:35 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.out b/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err b/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err deleted file mode 100644 index 4ce04d8..0000000 --- a/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:10:53 2024] -localrule chipr: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_log.txt - log: RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D6_log.out, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D6_log.err - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, FORM=narrow, IP_NAME=ATAC_D6 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak -m 2 --rankmethod signalvalue -o RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE > RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D6_log.out 2> RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D6_log.err - - -Activating singularity image epeak.sif -[Thu Sep 12 12:27:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.out b/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err b/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err deleted file mode 100644 index 11e91ee..0000000 --- a/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:11:02 2024] -localrule chipr: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_log.txt - log: RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D6F_log.out, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D6F_log.err - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, FORM=narrow, IP_NAME=ATAC_D6F - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak -m 2 --rankmethod signalvalue -o RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE > RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D6F_log.out 2> RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/logs/ATAC_D6F_log.err - - -Activating singularity image epeak.sif -[Thu Sep 12 12:28:31 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.out b/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shCtrl.err b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shCtrl.err deleted file mode 100644 index 0ca8cb6..0000000 --- a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shCtrl.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 17:06:39 2024] -localrule chipr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shCtrl_DONE_optimal.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shCtrl_DONE_all.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shCtrl_DONE_log.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/H3K27ac_shCtrl_log, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/H3K27ac_shCtrl_log_err - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=H3K27ac, COND=shCtrl - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak -m 2 -o chipr_tmp > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/H3K27ac_shCtrl_log 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/H3K27ac_shCtrl_log_err - mv chipr_tmp_optimal.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shCtrl_DONE_optimal.bed - mv chipr_tmp_all.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shCtrl_DONE_all.bed - mv chipr_tmp_log.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shCtrl_DONE_log.txt - -Activating singularity image epeak.sif -[Thu Sep 5 17:10:47 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shCtrl.out b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shCtrl.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shUbc9.err b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shUbc9.err deleted file mode 100644 index 498546d..0000000 --- a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shUbc9.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 17:22:36 2024] -localrule chipr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shUbc9_DONE_optimal.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shUbc9_DONE_all.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shUbc9_DONE_log.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/H3K27ac_shUbc9_log, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/H3K27ac_shUbc9_log_err - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=H3K27ac, COND=shUbc9 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak -m 2 -o chipr_tmp > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/H3K27ac_shUbc9_log 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/H3K27ac_shUbc9_log_err - mv chipr_tmp_optimal.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shUbc9_DONE_optimal.bed - mv chipr_tmp_all.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shUbc9_DONE_all.bed - mv chipr_tmp_log.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/H3K27ac_shUbc9_DONE_log.txt - -Activating singularity image epeak.sif -[Thu Sep 5 17:26:07 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shUbc9.out b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shUbc9.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shCtrl.err b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shCtrl.err deleted file mode 100644 index 40d59f6..0000000 --- a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shCtrl.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 17:08:30 2024] -localrule chipr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shCtrl_DONE_optimal.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shCtrl_DONE_all.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shCtrl_DONE_log.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/Klf4_shCtrl_log, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/Klf4_shCtrl_log_err - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=Klf4, COND=shCtrl - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak -m 2 -o chipr_tmp > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/Klf4_shCtrl_log 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/Klf4_shCtrl_log_err - mv chipr_tmp_optimal.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shCtrl_DONE_optimal.bed - mv chipr_tmp_all.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shCtrl_DONE_all.bed - mv chipr_tmp_log.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shCtrl_DONE_log.txt - -Activating singularity image epeak.sif -[Thu Sep 5 17:12:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shCtrl.out b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shCtrl.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shUbc9.err b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shUbc9.err deleted file mode 100644 index 9f69168..0000000 --- a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shUbc9.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 19:29:36 2024] -localrule chipr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shUbc9_DONE_optimal.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shUbc9_DONE_all.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shUbc9_DONE_log.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/Klf4_shUbc9_log, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/Klf4_shUbc9_log_err - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=Klf4, COND=shUbc9 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak -m 2 -o chipr_tmp > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/Klf4_shUbc9_log 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/logs/Klf4_shUbc9_log_err - mv chipr_tmp_optimal.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shUbc9_DONE_optimal.bed - mv chipr_tmp_all.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shUbc9_DONE_all.bed - mv chipr_tmp_log.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/Klf4_shUbc9_DONE_log.txt - -Activating singularity image epeak.sif -[Thu Sep 5 19:32:51 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shUbc9.out b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shUbc9.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D0.err b/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D0.err deleted file mode 100644 index b06a948..0000000 --- a/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D0.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:42:53 2024] -localrule chipr: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_log.txt - log: RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D0_log.out, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D0_log.err - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, FORM=narrow, IP_NAME=ATAC_D0 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak -m 2 --rankmethod signalvalue -o RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE > RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D0_log.out 2> RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D0_log.err - - -Activating singularity image epeak.sif -[Thu Sep 12 11:57:20 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D0.out b/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D0.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6.err b/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6.err deleted file mode 100644 index 6980cbe..0000000 --- a/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:42:53 2024] -localrule chipr: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_log.txt - log: RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D6_log.out, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D6_log.err - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, FORM=narrow, IP_NAME=ATAC_D6 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak -m 2 --rankmethod signalvalue -o RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE > RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D6_log.out 2> RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D6_log.err - - -Activating singularity image epeak.sif -[Thu Sep 12 11:57:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6.out b/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6F.err b/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6F.err deleted file mode 100644 index 6fcf97f..0000000 --- a/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6F.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:42:53 2024] -localrule chipr: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_log.txt - log: RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D6F_log.out, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D6F_log.err - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, FORM=narrow, IP_NAME=ATAC_D6F - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - chipr -i RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak -m 2 --rankmethod signalvalue -o RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE > RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D6F_log.out 2> RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/logs/ATAC_D6F_log.err - - -Activating singularity image epeak.sif -[Thu Sep 12 11:57:15 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6F.out b/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6F.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 4956176..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:35:08 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep1_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep1_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shCtrl_Rep1_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep1_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep1_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shCtrl_Rep1_mm10_matrix.out - -Activating singularity image epeak.sif -[Wed Sep 11 23:20:09 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index e234d3a..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:34:05 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep2_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep2_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shCtrl_Rep2_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep2_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep2_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shCtrl_Rep2_mm10_matrix.out - -Activating singularity image epeak.sif -[Thu Sep 12 00:20:15 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index e99c029..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:02:11 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep1_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep1_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shUbc9_Rep1_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep1_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep1_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shUbc9_Rep1_mm10_matrix.out - -Activating singularity image epeak.sif -[Wed Sep 11 23:49:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 5d08c70..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:09:15 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep2_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep2_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shUbc9_Rep2_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep2_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep2_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shUbc9_Rep2_mm10_matrix.out - -Activating singularity image epeak.sif -[Wed Sep 11 22:54:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index b2fd2d0..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:38 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep1_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/INPUT_shCtrl_Rep1_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/INPUT_shCtrl_Rep1_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shCtrl_Rep1_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/INPUT_shCtrl_Rep1_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/INPUT_shCtrl_Rep1_mm10_matrix.out - -Activating singularity image epeak.sif -[Thu Sep 12 12:34:32 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index d48125f..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 17:03:39 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/12-IGV/INPUT_shCtrl_Rep2_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep2_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shCtrl_Rep2_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/12-IGV/INPUT_shCtrl_Rep2_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep2_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shCtrl_Rep2_mm10_matrix.out - -Activating singularity image epeak.sif -[Thu Sep 5 18:55:08 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 6f49fdc..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:16:51 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep1_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/INPUT_shUbc9_Rep1_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/INPUT_shUbc9_Rep1_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/INPUT_shUbc9_Rep1_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/INPUT_shUbc9_Rep1_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/INPUT_shUbc9_Rep1_mm10_matrix.out - -Activating singularity image epeak.sif -[Thu Sep 12 13:07:54 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 4b2bb0e..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 19:35:32 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/12-IGV/INPUT_shUbc9_Rep2_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep2_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shUbc9_Rep2_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/12-IGV/INPUT_shUbc9_Rep2_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep2_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shUbc9_Rep2_mm10_matrix.out - -Activating singularity image epeak.sif -[Thu Sep 5 21:21:00 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index de87112..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:48:16 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep1_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep1_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shCtrl_Rep1_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep1_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep1_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shCtrl_Rep1_mm10_matrix.out - -Activating singularity image epeak.sif -[Wed Sep 11 23:33:48 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index adc6faf..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:11:08 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep2_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep2_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shCtrl_Rep2_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep2_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep2_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shCtrl_Rep2_mm10_matrix.out - -Activating singularity image epeak.sif -[Wed Sep 11 22:55:43 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 78970cd..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep1_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep1_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shUbc9_Rep1_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep1_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep1_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shUbc9_Rep1_mm10_matrix.out - -Activating singularity image epeak.sif -[Thu Sep 12 00:56:13 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 034d530..0000000 --- a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:12 2024] -localrule computeMatrix: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep2_mm10_coverage.bw - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep2_mm10.mat.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shUbc9_Rep2_mm10_matrix.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=mm10 - resources: mem_mb=38147, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=40G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - computeMatrix scale-regions -S /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep2_mm10_coverage.bw -R test/annotation/Mus_musculus.GRCm39.111.gtf --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros -p 1 -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep2_mm10.mat.gz 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shUbc9_Rep2_mm10_matrix.out - -Activating singularity image epeak.sif -[Thu Sep 12 00:49:20 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.err b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.err deleted file mode 100644 index 156dfc0..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:10:12 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_PPR1vsPPR2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=H3K27ac_shCtrl, CASE=PPR - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_PPR1vsPPR2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_PPR1vsPPR2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:11:25 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.out b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.err b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.err deleted file mode 100644 index 9bb5a4f..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:10:10 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_Rep1vsRep2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=H3K27ac_shCtrl, CASE=Rep - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_Rep1vsRep2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_Rep1vsRep2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:11:10 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.out b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..err b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..err deleted file mode 100644 index 3ad593a..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:10:10 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1vsSPR1.2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=H3K27ac_shCtrl, CASE=SPR1. - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1vsSPR1.2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1vsSPR1.2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:11:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..out b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..err b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..err deleted file mode 100644 index ce5e5a6..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:09:09 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1vsSPR2.2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=H3K27ac_shCtrl, CASE=SPR2. - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1vsSPR2.2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1vsSPR2.2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:10:44 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..out b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.err b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.err deleted file mode 100644 index db3f12b..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:10:42 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_PPR1vsPPR2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=H3K27ac_shUbc9, CASE=PPR - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_PPR1vsPPR2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_PPR1vsPPR2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:53 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.out b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.err b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.err deleted file mode 100644 index a328aaa..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:10:39 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_Rep1vsRep2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=H3K27ac_shUbc9, CASE=Rep - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_Rep1vsRep2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_Rep1vsRep2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:36 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.out b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..err b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..err deleted file mode 100644 index 81d445b..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:09:54 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1vsSPR1.2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=H3K27ac_shUbc9, CASE=SPR1. - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1vsSPR1.2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1vsSPR1.2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:12 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..out b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..err b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..err deleted file mode 100644 index 651a396..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:09:51 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1vsSPR2.2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=H3K27ac_shUbc9, CASE=SPR2. - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1vsSPR2.2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1vsSPR2.2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:56 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..out b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.err b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.err deleted file mode 100644 index 94105ab..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:11:42 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_PPR1vsPPR2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=Klf4_shCtrl, CASE=PPR - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_PPR1vsPPR2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_PPR1vsPPR2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:13:38 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.out b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.err b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.err deleted file mode 100644 index 08b4a0c..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:10:42 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_Rep1vsRep2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=Klf4_shCtrl, CASE=Rep - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_Rep1vsRep2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_Rep1vsRep2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:57 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.out b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..err b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..err deleted file mode 100644 index e6e438a..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:10:12 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_SPR1.1vsSPR1.2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=Klf4_shCtrl, CASE=SPR1. - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_SPR1.1vsSPR1.2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_SPR1.1vsSPR1.2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:10:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..out b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..err b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..err deleted file mode 100644 index 5dc8655..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:09:54 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_SPR2.1vsSPR2.2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=Klf4_shCtrl, CASE=SPR2. - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_SPR2.1vsSPR2.2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shCtrl_SPR2.1vsSPR2.2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:10:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..out b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.err b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.err deleted file mode 100644 index 5399acb..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:13:42 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_PPR1vsPPR2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=Klf4_shUbc9, CASE=PPR - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_PPR1vsPPR2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_PPR1vsPPR2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:14:47 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.out b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.err b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.err deleted file mode 100644 index 1dc12ee..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:14:45 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_Rep1vsRep2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=Klf4_shUbc9, CASE=Rep - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_Rep1vsRep2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_Rep1vsRep2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:15:48 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.out b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..err b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..err deleted file mode 100644 index f56337e..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:10:39 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_SPR1.1vsSPR1.2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=Klf4_shUbc9, CASE=SPR1. - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_SPR1.1vsSPR1.2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_SPR1.1vsSPR1.2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..out b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..err b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..err deleted file mode 100644 index 9a15578..0000000 --- a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..err +++ /dev/null @@ -1,52 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:12:51 2024] -localrule compute_idr: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr.txt, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_SPR2.1vsSPR2.2_narrow_idr.out - jobid: 0 - reason: Forced execution - wildcards: IP_IDR=Klf4_shUbc9, CASE=SPR2. - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - nb_peak1=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.1_peaks.narrowPeak | cut -d' ' -f1) - nb_peak2=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.2_peaks.narrowPeak | cut -d' ' -f1) - if [[ $nb_peak1 -gt 20 || $nb_peak2 -gt 20 ]] ; then - - #create temporary file for file1 and file2 - file1=$(mktemp) - file2=$(mktemp) - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.1_peaks.narrowPeak | head -100000 > $file1 - sort -k 7nr,7nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.2_peaks.narrowPeak | head -100000 > $file2 - - idr --samples $file1 $file2 --input-file-type narrowPeak --output-file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr.txt --rank signal.value --soft-idr-threshold 0.05 --plot 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_SPR2.1vsSPR2.2_narrow_idr.out - - IDR_tr=$(awk -v p=0.05 'BEGIN{print -log(p)/log(10)}') - awk -v x=$IDR_tr 'BEGIN{OFS=" "} $12>=x ' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr.txt | sort | uniq | sort -k7n,7n > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - else - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr.txt - touch /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - echo "ValueError: Peak files must contain at least 20 peaks post-merge" 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/Klf4_shUbc9_SPR2.1vsSPR2.2_narrow_idr.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:13:44 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..out b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.err deleted file mode 100644 index 5884304..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12864, disk_mib=12269, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:36 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep1_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep1_R2_001.fastq.gz - output: RES_ATAC/01-Trimming/ATAC_D0_rep1_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D0_rep1_R2_001_trim.fastq.gz - log: RES_ATAC/01-Trimming/logs/ATAC_D0_rep1_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1 - resources: mem_mb=9537, mem_mib=7630, disk_mb=12864, disk_mib=12269, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep1_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep1_R2_001.fastq.gz" - infiles=($tmp) - - tmp="RES_ATAC/01-Trimming/ATAC_D0_rep1_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D0_rep1_R2_001_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt_atac.fa -m 35 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - cmd+=" -${mode^^} file:config/adapt_atac.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - - #run command - eval "${cmd} > RES_ATAC/01-Trimming/logs/ATAC_D0_rep1_trim.txt" - - -Activating singularity image epeak.sif -[Wed Sep 11 16:20:05 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.err deleted file mode 100644 index 36eae4c..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=11222, disk_mib=10703, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:39 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep2_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep2_R2_001.fastq.gz - output: RES_ATAC/01-Trimming/ATAC_D0_rep2_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D0_rep2_R2_001_trim.fastq.gz - log: RES_ATAC/01-Trimming/logs/ATAC_D0_rep2_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=11222, disk_mib=10703, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep2_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep2_R2_001.fastq.gz" - infiles=($tmp) - - tmp="RES_ATAC/01-Trimming/ATAC_D0_rep2_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D0_rep2_R2_001_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt_atac.fa -m 35 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - cmd+=" -${mode^^} file:config/adapt_atac.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - - #run command - eval "${cmd} > RES_ATAC/01-Trimming/logs/ATAC_D0_rep2_trim.txt" - - -Activating singularity image epeak.sif -[Wed Sep 11 16:16:06 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.err deleted file mode 100644 index e2a5166..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10287, disk_mib=9811, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:36 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R2_001.fastq.gz - output: RES_ATAC/01-Trimming/ATAC_D0_rep3_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D0_rep3_R2_001_trim.fastq.gz - log: RES_ATAC/01-Trimming/logs/ATAC_D0_rep3_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3 - resources: mem_mb=9537, mem_mib=7630, disk_mb=10287, disk_mib=9811, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R2_001.fastq.gz" - infiles=($tmp) - - tmp="RES_ATAC/01-Trimming/ATAC_D0_rep3_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D0_rep3_R2_001_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt_atac.fa -m 35 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - cmd+=" -${mode^^} file:config/adapt_atac.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - - #run command - eval "${cmd} > RES_ATAC/01-Trimming/logs/ATAC_D0_rep3_trim.txt" - - -Activating singularity image epeak.sif -[Wed Sep 11 16:12:45 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.err deleted file mode 100644 index 2e601c1..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5353, disk_mb=5613, disk_mib=5353, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:41 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R2_001.fastq.gz - output: RES_ATAC/01-Trimming/ATAC_D6F_rep1_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6F_rep1_R2_001_trim.fastq.gz - log: RES_ATAC/01-Trimming/logs/ATAC_D6F_rep1_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1 - resources: mem_mb=9537, mem_mib=5353, disk_mb=5613, disk_mib=5353, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R2_001.fastq.gz" - infiles=($tmp) - - tmp="RES_ATAC/01-Trimming/ATAC_D6F_rep1_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6F_rep1_R2_001_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt_atac.fa -m 35 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - cmd+=" -${mode^^} file:config/adapt_atac.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - - #run command - eval "${cmd} > RES_ATAC/01-Trimming/logs/ATAC_D6F_rep1_trim.txt" - - -Activating singularity image epeak.sif -[Wed Sep 11 15:59:16 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.err deleted file mode 100644 index c7dca85..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5374, disk_mb=5635, disk_mib=5374, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:41 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep2_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep2_R2_001.fastq.gz - output: RES_ATAC/01-Trimming/ATAC_D6F_rep2_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6F_rep2_R2_001_trim.fastq.gz - log: RES_ATAC/01-Trimming/logs/ATAC_D6F_rep2_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2 - resources: mem_mb=9537, mem_mib=5374, disk_mb=5635, disk_mib=5374, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep2_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep2_R2_001.fastq.gz" - infiles=($tmp) - - tmp="RES_ATAC/01-Trimming/ATAC_D6F_rep2_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6F_rep2_R2_001_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt_atac.fa -m 35 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - cmd+=" -${mode^^} file:config/adapt_atac.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - - #run command - eval "${cmd} > RES_ATAC/01-Trimming/logs/ATAC_D6F_rep2_trim.txt" - - -Activating singularity image epeak.sif -[Wed Sep 11 15:59:38 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.err deleted file mode 100644 index a44ab04..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6498, disk_mb=6813, disk_mib=6498, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:41 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep3_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep3_R2_001.fastq.gz - output: RES_ATAC/01-Trimming/ATAC_D6F_rep3_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6F_rep3_R2_001_trim.fastq.gz - log: RES_ATAC/01-Trimming/logs/ATAC_D6F_rep3_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3 - resources: mem_mb=9537, mem_mib=6498, disk_mb=6813, disk_mib=6498, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep3_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep3_R2_001.fastq.gz" - infiles=($tmp) - - tmp="RES_ATAC/01-Trimming/ATAC_D6F_rep3_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6F_rep3_R2_001_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt_atac.fa -m 35 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - cmd+=" -${mode^^} file:config/adapt_atac.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - - #run command - eval "${cmd} > RES_ATAC/01-Trimming/logs/ATAC_D6F_rep3_trim.txt" - - -Activating singularity image epeak.sif -[Wed Sep 11 16:02:25 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.err deleted file mode 100644 index 009b830..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5798, disk_mb=6079, disk_mib=5798, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:39 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep1_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep1_R2_001.fastq.gz - output: RES_ATAC/01-Trimming/ATAC_D6_rep1_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6_rep1_R2_001_trim.fastq.gz - log: RES_ATAC/01-Trimming/logs/ATAC_D6_rep1_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1 - resources: mem_mb=9537, mem_mib=5798, disk_mb=6079, disk_mib=5798, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep1_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep1_R2_001.fastq.gz" - infiles=($tmp) - - tmp="RES_ATAC/01-Trimming/ATAC_D6_rep1_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6_rep1_R2_001_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt_atac.fa -m 35 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - cmd+=" -${mode^^} file:config/adapt_atac.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - - #run command - eval "${cmd} > RES_ATAC/01-Trimming/logs/ATAC_D6_rep1_trim.txt" - - -Activating singularity image epeak.sif -[Wed Sep 11 16:00:17 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.err deleted file mode 100644 index 8445e80..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=8091, disk_mib=7717, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:36 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep2_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep2_R2_001.fastq.gz - output: RES_ATAC/01-Trimming/ATAC_D6_rep2_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6_rep2_R2_001_trim.fastq.gz - log: RES_ATAC/01-Trimming/logs/ATAC_D6_rep2_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=8091, disk_mib=7717, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep2_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep2_R2_001.fastq.gz" - infiles=($tmp) - - tmp="RES_ATAC/01-Trimming/ATAC_D6_rep2_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6_rep2_R2_001_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt_atac.fa -m 35 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - cmd+=" -${mode^^} file:config/adapt_atac.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - - #run command - eval "${cmd} > RES_ATAC/01-Trimming/logs/ATAC_D6_rep2_trim.txt" - - -Activating singularity image epeak.sif -[Wed Sep 11 16:05:48 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.err deleted file mode 100644 index 2169de3..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10759, disk_mib=10261, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:41 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep3_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep3_R2_001.fastq.gz - output: RES_ATAC/01-Trimming/ATAC_D6_rep3_R1_001_trim.fastq.gz, RES_ATAC/01-Trimming/ATAC_D6_rep3_R2_001_trim.fastq.gz - log: RES_ATAC/01-Trimming/logs/ATAC_D6_rep3_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3 - resources: mem_mb=9537, mem_mib=7630, disk_mb=10759, disk_mib=10261, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep3_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep3_R2_001.fastq.gz" - infiles=($tmp) - - tmp="RES_ATAC/01-Trimming/ATAC_D6_rep3_R1_001_trim.fastq.gz RES_ATAC/01-Trimming/ATAC_D6_rep3_R2_001_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt_atac.fa -m 35 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; then - cmd+=" -${mode^^} file:config/adapt_atac.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - - #run command - eval "${cmd} > RES_ATAC/01-Trimming/logs/ATAC_D6_rep3_trim.txt" - - -Activating singularity image epeak.sif -[Wed Sep 11 16:14:10 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.err deleted file mode 100644 index ebea041..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4948, disk_mb=5188, disk_mib=4948, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:01 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shCtrl_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep1_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/H3K27ac_shCtrl_Rep1_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=4948, disk_mb=5188, disk_mib=4948, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shCtrl_Rep1_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep1_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/H3K27ac_shCtrl_Rep1_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:18:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.err deleted file mode 100644 index 806416d..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5218, disk_mb=5471, disk_mib=5218, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:05 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shCtrl_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep2_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/H3K27ac_shCtrl_Rep2_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=5218, disk_mb=5471, disk_mib=5218, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shCtrl_Rep2_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shCtrl_Rep2_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/H3K27ac_shCtrl_Rep2_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:19:17 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.err deleted file mode 100644 index 7d24ea3..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5906, disk_mb=6192, disk_mib=5906, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:08 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shUbc9_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep1_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/H3K27ac_shUbc9_Rep1_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=5906, disk_mb=6192, disk_mib=5906, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shUbc9_Rep1_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep1_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/H3K27ac_shUbc9_Rep1_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:22:18 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.err deleted file mode 100644 index 7adc736..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4599, disk_mb=4822, disk_mib=4599, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:05 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shUbc9_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep2_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/H3K27ac_shUbc9_Rep2_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=4599, disk_mb=4822, disk_mib=4599, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shUbc9_Rep2_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/H3K27ac_shUbc9_Rep2_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/H3K27ac_shUbc9_Rep2_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:15:38 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.err deleted file mode 100644 index 966fe7e..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4264, disk_mb=4471, disk_mib=4264, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:05 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shCtrl_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep1_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/INPUT_shCtrl_Rep1_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=4264, disk_mb=4471, disk_mib=4264, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shCtrl_Rep1_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep1_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/INPUT_shCtrl_Rep1_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:16:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.err deleted file mode 100644 index 31b1196..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4858, disk_mb=5093, disk_mib=4858, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:01 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shCtrl_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep2_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/INPUT_shCtrl_Rep2_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=4858, disk_mb=5093, disk_mib=4858, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shCtrl_Rep2_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shCtrl_Rep2_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/INPUT_shCtrl_Rep2_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:19:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.err deleted file mode 100644 index b74c512..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4879, disk_mb=5116, disk_mib=4879, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:05 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shUbc9_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep1_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/INPUT_shUbc9_Rep1_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=4879, disk_mb=5116, disk_mib=4879, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shUbc9_Rep1_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep1_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/INPUT_shUbc9_Rep1_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:19:58 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.err deleted file mode 100644 index c9e7497..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5208, disk_mb=5460, disk_mib=5208, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:01 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shUbc9_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep2_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/INPUT_shUbc9_Rep2_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=5208, disk_mb=5460, disk_mib=5208, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shUbc9_Rep2_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/INPUT_shUbc9_Rep2_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/INPUT_shUbc9_Rep2_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:21:57 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.err deleted file mode 100644 index 7d14809..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4153, disk_mb=4354, disk_mib=4153, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:09 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shCtrl_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep1_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/Klf4_shCtrl_Rep1_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=4153, disk_mb=4354, disk_mib=4153, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shCtrl_Rep1_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep1_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/Klf4_shCtrl_Rep1_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:16:45 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.err deleted file mode 100644 index b664165..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3793, disk_mb=3977, disk_mib=3793, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:09 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shCtrl_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep2_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/Klf4_shCtrl_Rep2_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=3793, disk_mb=3977, disk_mib=3793, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shCtrl_Rep2_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shCtrl_Rep2_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/Klf4_shCtrl_Rep2_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:13:59 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.err deleted file mode 100644 index 2885a3c..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4285, disk_mb=4493, disk_mib=4285, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:08 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shUbc9_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep1_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/Klf4_shUbc9_Rep1_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=4285, disk_mb=4493, disk_mib=4285, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shUbc9_Rep1_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep1_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/Klf4_shUbc9_Rep1_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:16:53 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.err deleted file mode 100644 index 80c06a8..0000000 --- a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.err +++ /dev/null @@ -1,54 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5197, disk_mb=5449, disk_mib=5197, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:05 2024] -localrule cutadapt: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shUbc9_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep2_R1_trim.fastq.gz - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/Klf4_shUbc9_Rep2_trim.txt - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=5197, disk_mb=5449, disk_mib=5197, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shUbc9_Rep2_R1.fastq.gz" - infiles=($tmp) - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/Klf4_shUbc9_Rep2_R1_trim.fastq.gz" - outfiles=($tmp) - - mode="a" - - # add mode and adapter sequences - cmd+=" cutadapt -${mode} file:config/adapt.fa -m 25 -q 30 -O 6 --trim-n --max-n 1 -j 1 " - # paired end or single end - if [[ ${#infiles[@]} -eq 2 ]]; - then - cmd+=" -${mode^^} file:config/adapt.fa -o ${outfiles[0]} -p ${outfiles[1]} ${infiles[0]} ${infiles[1]} " - else - cmd+=" -o ${outfiles[0]} ${infiles[0]}" - fi - #run command - eval "${cmd} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/01-Trimming/logs/Klf4_shUbc9_Rep2_trim.txt" - - -Activating singularity image epeak.sif -Adapter 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' (regular 3') was specified multiple times! Please make sure that this is what you want. -[Wed Sep 11 16:23:00 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.out b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.err deleted file mode 100644 index 07f4278..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.err +++ /dev/null @@ -1,71 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12864, disk_mib=12269, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:36 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep1_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep1_R2_001.fastq.gz - output: RES_ATAC/00-Fastqc/ATAC_D0_rep1_R1_001_fastqc.done - log: RES_ATAC/00-Fastqc/logs/ATAC_D0_rep1_R1_001_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1 - resources: mem_mb=9537, mem_mib=7630, disk_mb=12864, disk_mib=12269, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep1_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep1_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D0_rep1_R1_001_fastqc_raw.log - -Activating singularity image epeak.sif -Started analysis of ATAC_D0_rep1_R1_001.fastq.gz -Approx 5% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 10% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 15% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 20% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 25% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 30% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 35% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 40% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 45% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 50% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 55% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 60% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 65% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 70% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 75% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 80% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 85% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 90% complete for ATAC_D0_rep1_R1_001.fastq.gz -Approx 95% complete for ATAC_D0_rep1_R1_001.fastq.gz -Started analysis of ATAC_D0_rep1_R2_001.fastq.gz -Approx 5% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 10% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 15% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 20% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 25% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 30% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 35% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 40% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 45% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 50% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 55% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 60% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 65% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 70% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 75% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 80% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 85% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 90% complete for ATAC_D0_rep1_R2_001.fastq.gz -Approx 95% complete for ATAC_D0_rep1_R2_001.fastq.gz -Touching output file RES_ATAC/00-Fastqc/ATAC_D0_rep1_R1_001_fastqc.done. -[Wed Sep 11 15:56:11 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.err deleted file mode 100644 index f47c73b..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.err +++ /dev/null @@ -1,71 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=11222, disk_mib=10703, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:41 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep2_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep2_R2_001.fastq.gz - output: RES_ATAC/00-Fastqc/ATAC_D0_rep2_R1_001_fastqc.done - log: RES_ATAC/00-Fastqc/logs/ATAC_D0_rep2_R1_001_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=11222, disk_mib=10703, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep2_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep2_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D0_rep2_R1_001_fastqc_raw.log - -Activating singularity image epeak.sif -Started analysis of ATAC_D0_rep2_R1_001.fastq.gz -Approx 5% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 10% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 15% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 20% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 25% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 30% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 35% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 40% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 45% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 50% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 55% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 60% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 65% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 70% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 75% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 80% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 85% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 90% complete for ATAC_D0_rep2_R1_001.fastq.gz -Approx 95% complete for ATAC_D0_rep2_R1_001.fastq.gz -Started analysis of ATAC_D0_rep2_R2_001.fastq.gz -Approx 5% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 10% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 15% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 20% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 25% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 30% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 35% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 40% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 45% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 50% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 55% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 60% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 65% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 70% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 75% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 80% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 85% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 90% complete for ATAC_D0_rep2_R2_001.fastq.gz -Approx 95% complete for ATAC_D0_rep2_R2_001.fastq.gz -Touching output file RES_ATAC/00-Fastqc/ATAC_D0_rep2_R1_001_fastqc.done. -[Wed Sep 11 15:53:59 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.err deleted file mode 100644 index 1514eed..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.err +++ /dev/null @@ -1,71 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10287, disk_mib=9811, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:39 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R2_001.fastq.gz - output: RES_ATAC/00-Fastqc/ATAC_D0_rep3_R1_001_fastqc.done - log: RES_ATAC/00-Fastqc/logs/ATAC_D0_rep3_R1_001_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3 - resources: mem_mb=9537, mem_mib=7630, disk_mb=10287, disk_mib=9811, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D0_rep3_R1_001_fastqc_raw.log - -Activating singularity image epeak.sif -Started analysis of ATAC_D0_rep3_R1_001.fastq.gz -Approx 5% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 10% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 15% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 20% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 25% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 30% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 35% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 40% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 45% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 50% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 55% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 60% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 65% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 70% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 75% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 80% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 85% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 90% complete for ATAC_D0_rep3_R1_001.fastq.gz -Approx 95% complete for ATAC_D0_rep3_R1_001.fastq.gz -Started analysis of ATAC_D0_rep3_R2_001.fastq.gz -Approx 5% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 10% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 15% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 20% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 25% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 30% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 35% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 40% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 45% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 50% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 55% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 60% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 65% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 70% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 75% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 80% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 85% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 90% complete for ATAC_D0_rep3_R2_001.fastq.gz -Approx 95% complete for ATAC_D0_rep3_R2_001.fastq.gz -Touching output file RES_ATAC/00-Fastqc/ATAC_D0_rep3_R1_001_fastqc.done. -[Wed Sep 11 15:53:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.err deleted file mode 100644 index d468be2..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.err +++ /dev/null @@ -1,71 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5353, disk_mb=5613, disk_mib=5353, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:41 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R2_001.fastq.gz - output: RES_ATAC/00-Fastqc/ATAC_D6F_rep1_R1_001_fastqc.done - log: RES_ATAC/00-Fastqc/logs/ATAC_D6F_rep1_R1_001_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1 - resources: mem_mb=9537, mem_mib=5353, disk_mb=5613, disk_mib=5353, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D6F_rep1_R1_001_fastqc_raw.log - -Activating singularity image epeak.sif -Started analysis of ATAC_D6F_rep1_R1_001.fastq.gz -Approx 5% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 10% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 15% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 20% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 25% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 30% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 35% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 40% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 45% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 50% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 55% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 60% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 65% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 70% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 75% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 80% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 85% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 90% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Approx 95% complete for ATAC_D6F_rep1_R1_001.fastq.gz -Started analysis of ATAC_D6F_rep1_R2_001.fastq.gz -Approx 5% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 10% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 15% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 20% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 25% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 30% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 35% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 40% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 45% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 50% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 55% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 60% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 65% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 70% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 75% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 80% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 85% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 90% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Approx 95% complete for ATAC_D6F_rep1_R2_001.fastq.gz -Touching output file RES_ATAC/00-Fastqc/ATAC_D6F_rep1_R1_001_fastqc.done. -[Wed Sep 11 15:50:11 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.err deleted file mode 100644 index 440dc14..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.err +++ /dev/null @@ -1,71 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5374, disk_mb=5635, disk_mib=5374, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:36 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep2_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep2_R2_001.fastq.gz - output: RES_ATAC/00-Fastqc/ATAC_D6F_rep2_R1_001_fastqc.done - log: RES_ATAC/00-Fastqc/logs/ATAC_D6F_rep2_R1_001_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2 - resources: mem_mb=9537, mem_mib=5374, disk_mb=5635, disk_mib=5374, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep2_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep2_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D6F_rep2_R1_001_fastqc_raw.log - -Activating singularity image epeak.sif -Started analysis of ATAC_D6F_rep2_R1_001.fastq.gz -Approx 5% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 10% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 15% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 20% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 25% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 30% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 35% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 40% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 45% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 50% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 55% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 60% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 65% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 70% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 75% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 80% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 85% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 90% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Approx 95% complete for ATAC_D6F_rep2_R1_001.fastq.gz -Started analysis of ATAC_D6F_rep2_R2_001.fastq.gz -Approx 5% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 10% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 15% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 20% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 25% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 30% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 35% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 40% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 45% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 50% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 55% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 60% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 65% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 70% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 75% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 80% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 85% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 90% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Approx 95% complete for ATAC_D6F_rep2_R2_001.fastq.gz -Touching output file RES_ATAC/00-Fastqc/ATAC_D6F_rep2_R1_001_fastqc.done. -[Wed Sep 11 15:50:05 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.err deleted file mode 100644 index cd70221..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.err +++ /dev/null @@ -1,71 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6498, disk_mb=6813, disk_mib=6498, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:41 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep3_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep3_R2_001.fastq.gz - output: RES_ATAC/00-Fastqc/ATAC_D6F_rep3_R1_001_fastqc.done - log: RES_ATAC/00-Fastqc/logs/ATAC_D6F_rep3_R1_001_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3 - resources: mem_mb=9537, mem_mib=6498, disk_mb=6813, disk_mib=6498, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep3_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep3_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D6F_rep3_R1_001_fastqc_raw.log - -Activating singularity image epeak.sif -Started analysis of ATAC_D6F_rep3_R1_001.fastq.gz -Approx 5% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 10% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 15% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 20% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 25% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 30% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 35% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 40% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 45% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 50% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 55% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 60% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 65% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 70% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 75% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 80% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 85% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 90% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Approx 95% complete for ATAC_D6F_rep3_R1_001.fastq.gz -Started analysis of ATAC_D6F_rep3_R2_001.fastq.gz -Approx 5% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 10% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 15% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 20% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 25% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 30% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 35% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 40% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 45% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 50% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 55% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 60% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 65% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 70% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 75% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 80% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 85% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 90% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Approx 95% complete for ATAC_D6F_rep3_R2_001.fastq.gz -Touching output file RES_ATAC/00-Fastqc/ATAC_D6F_rep3_R1_001_fastqc.done. -[Wed Sep 11 15:50:55 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.err deleted file mode 100644 index cce2e7e..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.err +++ /dev/null @@ -1,71 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5798, disk_mb=6079, disk_mib=5798, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:36 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep1_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep1_R2_001.fastq.gz - output: RES_ATAC/00-Fastqc/ATAC_D6_rep1_R1_001_fastqc.done - log: RES_ATAC/00-Fastqc/logs/ATAC_D6_rep1_R1_001_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1 - resources: mem_mb=9537, mem_mib=5798, disk_mb=6079, disk_mib=5798, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep1_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep1_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D6_rep1_R1_001_fastqc_raw.log - -Activating singularity image epeak.sif -Started analysis of ATAC_D6_rep1_R1_001.fastq.gz -Approx 5% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 10% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 15% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 20% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 25% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 30% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 35% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 40% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 45% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 50% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 55% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 60% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 65% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 70% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 75% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 80% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 85% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 90% complete for ATAC_D6_rep1_R1_001.fastq.gz -Approx 95% complete for ATAC_D6_rep1_R1_001.fastq.gz -Started analysis of ATAC_D6_rep1_R2_001.fastq.gz -Approx 5% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 10% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 15% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 20% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 25% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 30% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 35% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 40% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 45% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 50% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 55% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 60% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 65% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 70% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 75% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 80% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 85% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 90% complete for ATAC_D6_rep1_R2_001.fastq.gz -Approx 95% complete for ATAC_D6_rep1_R2_001.fastq.gz -Touching output file RES_ATAC/00-Fastqc/ATAC_D6_rep1_R1_001_fastqc.done. -[Wed Sep 11 15:50:25 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.err deleted file mode 100644 index 59447b3..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.err +++ /dev/null @@ -1,71 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=8091, disk_mib=7717, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:41 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep2_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep2_R2_001.fastq.gz - output: RES_ATAC/00-Fastqc/ATAC_D6_rep2_R1_001_fastqc.done - log: RES_ATAC/00-Fastqc/logs/ATAC_D6_rep2_R1_001_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=8091, disk_mib=7717, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep2_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep2_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D6_rep2_R1_001_fastqc_raw.log - -Activating singularity image epeak.sif -Started analysis of ATAC_D6_rep2_R1_001.fastq.gz -Approx 5% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 10% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 15% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 20% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 25% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 30% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 35% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 40% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 45% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 50% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 55% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 60% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 65% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 70% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 75% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 80% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 85% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 90% complete for ATAC_D6_rep2_R1_001.fastq.gz -Approx 95% complete for ATAC_D6_rep2_R1_001.fastq.gz -Started analysis of ATAC_D6_rep2_R2_001.fastq.gz -Approx 5% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 10% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 15% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 20% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 25% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 30% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 35% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 40% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 45% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 50% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 55% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 60% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 65% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 70% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 75% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 80% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 85% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 90% complete for ATAC_D6_rep2_R2_001.fastq.gz -Approx 95% complete for ATAC_D6_rep2_R2_001.fastq.gz -Touching output file RES_ATAC/00-Fastqc/ATAC_D6_rep2_R1_001_fastqc.done. -[Wed Sep 11 15:51:53 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.err deleted file mode 100644 index 97e58f3..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.err +++ /dev/null @@ -1,71 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10759, disk_mib=10261, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:45:41 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep3_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep3_R2_001.fastq.gz - output: RES_ATAC/00-Fastqc/ATAC_D6_rep3_R1_001_fastqc.done - log: RES_ATAC/00-Fastqc/logs/ATAC_D6_rep3_R1_001_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3 - resources: mem_mb=9537, mem_mib=7630, disk_mb=10759, disk_mib=10261, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep3_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6_rep3_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D6_rep3_R1_001_fastqc_raw.log - -Activating singularity image epeak.sif -Started analysis of ATAC_D6_rep3_R1_001.fastq.gz -Approx 5% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 10% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 15% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 20% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 25% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 30% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 35% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 40% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 45% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 50% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 55% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 60% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 65% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 70% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 75% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 80% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 85% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 90% complete for ATAC_D6_rep3_R1_001.fastq.gz -Approx 95% complete for ATAC_D6_rep3_R1_001.fastq.gz -Started analysis of ATAC_D6_rep3_R2_001.fastq.gz -Approx 5% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 10% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 15% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 20% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 25% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 30% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 35% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 40% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 45% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 50% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 55% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 60% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 65% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 70% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 75% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 80% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 85% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 90% complete for ATAC_D6_rep3_R2_001.fastq.gz -Approx 95% complete for ATAC_D6_rep3_R2_001.fastq.gz -Touching output file RES_ATAC/00-Fastqc/ATAC_D6_rep3_R1_001_fastqc.done. -[Wed Sep 11 15:53:56 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.err deleted file mode 100644 index da8544f..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4948, disk_mb=5188, disk_mib=4948, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:05 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shCtrl_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/H3K27ac_shCtrl_Rep1_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/H3K27ac_shCtrl_Rep1_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=4948, disk_mb=5188, disk_mib=4948, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shCtrl_Rep1_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/H3K27ac_shCtrl_Rep1_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 5% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 10% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 15% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 20% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 25% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 30% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 35% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 40% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 45% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 50% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 55% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 60% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 65% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 70% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 75% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 80% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 85% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 90% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Approx 95% complete for H3K27ac_shCtrl_Rep1_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/H3K27ac_shCtrl_Rep1_R1_fastqc.done. -[Wed Sep 11 15:55:06 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.err deleted file mode 100644 index e773920..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5218, disk_mb=5471, disk_mib=5218, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:05 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shCtrl_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/H3K27ac_shCtrl_Rep2_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/H3K27ac_shCtrl_Rep2_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=5218, disk_mb=5471, disk_mib=5218, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shCtrl_Rep2_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/H3K27ac_shCtrl_Rep2_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 5% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 10% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 15% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 20% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 25% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 30% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 35% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 40% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 45% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 50% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 55% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 60% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 65% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 70% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 75% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 80% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 85% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 90% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Approx 95% complete for H3K27ac_shCtrl_Rep2_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/H3K27ac_shCtrl_Rep2_R1_fastqc.done. -[Wed Sep 11 15:55:09 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.out b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.err deleted file mode 100644 index f1df293..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5906, disk_mb=6192, disk_mib=5906, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:00 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shUbc9_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/H3K27ac_shUbc9_Rep1_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/H3K27ac_shUbc9_Rep1_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=5906, disk_mb=6192, disk_mib=5906, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shUbc9_Rep1_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/H3K27ac_shUbc9_Rep1_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 5% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 10% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 15% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 20% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 25% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 30% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 35% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 40% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 45% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 50% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 55% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 60% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 65% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 70% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 75% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 80% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 85% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 90% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Approx 95% complete for H3K27ac_shUbc9_Rep1_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/H3K27ac_shUbc9_Rep1_R1_fastqc.done. -[Wed Sep 11 15:55:28 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.err deleted file mode 100644 index 28bf78d..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4599, disk_mb=4822, disk_mib=4599, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:08 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shUbc9_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/H3K27ac_shUbc9_Rep2_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/H3K27ac_shUbc9_Rep2_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=4599, disk_mb=4822, disk_mib=4599, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/H3K27ac_shUbc9_Rep2_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/H3K27ac_shUbc9_Rep2_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 5% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 10% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 15% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 20% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 25% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 30% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 35% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 40% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 45% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 50% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 55% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 60% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 65% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 70% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 75% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 80% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 85% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 90% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Approx 95% complete for H3K27ac_shUbc9_Rep2_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/H3K27ac_shUbc9_Rep2_R1_fastqc.done. -[Wed Sep 11 15:54:48 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.out b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.err deleted file mode 100644 index d3c3515..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4264, disk_mb=4471, disk_mib=4264, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:08 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shCtrl_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/INPUT_shCtrl_Rep1_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/INPUT_shCtrl_Rep1_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=4264, disk_mb=4471, disk_mib=4264, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shCtrl_Rep1_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/INPUT_shCtrl_Rep1_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 5% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 10% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 15% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 20% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 25% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 30% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 35% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 40% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 45% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 50% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 55% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 60% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 65% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 70% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 75% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 80% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 85% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 90% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Approx 95% complete for INPUT_shCtrl_Rep1_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/INPUT_shCtrl_Rep1_R1_fastqc.done. -[Wed Sep 11 15:54:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.err deleted file mode 100644 index c30716d..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4858, disk_mb=5093, disk_mib=4858, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:05 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shCtrl_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/INPUT_shCtrl_Rep2_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/INPUT_shCtrl_Rep2_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=4858, disk_mb=5093, disk_mib=4858, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shCtrl_Rep2_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/INPUT_shCtrl_Rep2_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 5% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 10% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 15% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 20% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 25% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 30% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 35% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 40% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 45% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 50% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 55% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 60% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 65% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 70% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 75% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 80% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 85% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 90% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Approx 95% complete for INPUT_shCtrl_Rep2_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/INPUT_shCtrl_Rep2_R1_fastqc.done. -[Wed Sep 11 15:55:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.out b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.err deleted file mode 100644 index a91cb77..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4879, disk_mb=5116, disk_mib=4879, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:09 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shUbc9_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/INPUT_shUbc9_Rep1_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/INPUT_shUbc9_Rep1_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=4879, disk_mb=5116, disk_mib=4879, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shUbc9_Rep1_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/INPUT_shUbc9_Rep1_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 5% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 10% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 15% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 20% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 25% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 30% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 35% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 40% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 45% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 50% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 55% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 60% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 65% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 70% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 75% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 80% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 85% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 90% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Approx 95% complete for INPUT_shUbc9_Rep1_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/INPUT_shUbc9_Rep1_R1_fastqc.done. -[Wed Sep 11 15:55:02 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.err deleted file mode 100644 index 1e831a7..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5208, disk_mb=5460, disk_mib=5208, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:08 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shUbc9_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/INPUT_shUbc9_Rep2_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/INPUT_shUbc9_Rep2_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=5208, disk_mb=5460, disk_mib=5208, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/INPUT_shUbc9_Rep2_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/INPUT_shUbc9_Rep2_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 5% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 10% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 15% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 20% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 25% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 30% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 35% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 40% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 45% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 50% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 55% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 60% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 65% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 70% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 75% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 80% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 85% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 90% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Approx 95% complete for INPUT_shUbc9_Rep2_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/INPUT_shUbc9_Rep2_R1_fastqc.done. -[Wed Sep 11 15:55:32 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.out b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.err deleted file mode 100644 index fefffd8..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4153, disk_mb=4354, disk_mib=4153, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:08 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shCtrl_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/Klf4_shCtrl_Rep1_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/Klf4_shCtrl_Rep1_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=4153, disk_mb=4354, disk_mib=4153, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shCtrl_Rep1_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/Klf4_shCtrl_Rep1_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 5% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 10% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 15% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 20% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 25% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 30% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 35% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 40% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 45% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 50% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 55% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 60% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 65% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 70% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 75% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 80% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 85% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 90% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Approx 95% complete for Klf4_shCtrl_Rep1_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/Klf4_shCtrl_Rep1_R1_fastqc.done. -[Wed Sep 11 15:54:56 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.err deleted file mode 100644 index d735d03..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3793, disk_mb=3977, disk_mib=3793, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:08 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shCtrl_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/Klf4_shCtrl_Rep2_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/Klf4_shCtrl_Rep2_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=3793, disk_mb=3977, disk_mib=3793, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shCtrl_Rep2_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/Klf4_shCtrl_Rep2_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 5% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 10% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 15% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 20% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 25% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 30% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 35% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 40% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 45% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 50% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 55% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 60% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 65% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 70% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 75% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 80% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 85% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 90% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Approx 95% complete for Klf4_shCtrl_Rep2_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/Klf4_shCtrl_Rep2_R1_fastqc.done. -[Wed Sep 11 15:54:30 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.out b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.err deleted file mode 100644 index 83e7620..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4285, disk_mb=4493, disk_mib=4285, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:09 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shUbc9_Rep1_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/Klf4_shUbc9_Rep1_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/Klf4_shUbc9_Rep1_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=4285, disk_mb=4493, disk_mib=4285, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shUbc9_Rep1_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/Klf4_shUbc9_Rep1_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 5% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 10% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 15% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 20% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 25% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 30% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 35% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 40% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 45% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 50% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 55% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 60% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 65% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 70% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 75% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 80% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 85% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 90% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Approx 95% complete for Klf4_shUbc9_Rep1_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/Klf4_shUbc9_Rep1_R1_fastqc.done. -[Wed Sep 11 15:54:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.err deleted file mode 100644 index b76524e..0000000 --- a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.err +++ /dev/null @@ -1,51 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5197, disk_mb=5449, disk_mib=5197, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:51:05 2024] -localrule fastqc: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shUbc9_Rep2_R1.fastq.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/Klf4_shUbc9_Rep2_R1_fastqc.done - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/Klf4_shUbc9_Rep2_R1_fastqc_raw.log - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=5197, disk_mb=5449, disk_mib=5197, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -fastqc -t 1 --outdir /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/ePeak_old/data2/Klf4_shUbc9_Rep2_R1.fastq.gz > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/logs/Klf4_shUbc9_Rep2_R1_fastqc_raw.log -Activating singularity image epeak.sif -Started analysis of Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 5% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 10% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 15% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 20% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 25% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 30% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 35% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 40% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 45% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 50% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 55% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 60% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 65% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 70% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 75% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 80% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 85% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 90% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Approx 95% complete for Klf4_shUbc9_Rep2_R1.fastq.gz -Touching output file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/00-Fastqc/Klf4_shUbc9_Rep2_R1_fastqc.done. -[Wed Sep 11 15:55:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.out b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=genrich.MOD=narrow.MARK=ATAC.err b/logs/slurm/feature_counts/feature_counts_CALLER=genrich.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index 773fb20..0000000 --- a/logs/slurm/feature_counts/feature_counts_CALLER=genrich.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=69585, disk_mib=66362, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:27:07 2024] -localrule feature_counts: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff - output: RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_Matrix_Optimal_Peak.mtx - log: RES_ATAC/09-CountMatrix/genrich_narrow/logs/ATAC_counts.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=7630, disk_mb=69585, disk_mib=66362, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - featureCounts -T 1 -t peak -g gene_id -p -a RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff -o RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_Matrix_Optimal_Peak.mtx RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam 2> RES_ATAC/09-CountMatrix/genrich_narrow/logs/ATAC_counts.out - -Activating singularity image epeak.sif -[Thu Sep 12 12:42:23 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=genrich.MOD=narrow.MARK=ATAC.out b/logs/slurm/feature_counts/feature_counts_CALLER=genrich.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err b/logs/slurm/feature_counts/feature_counts_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index 0e458e0..0000000 --- a/logs/slurm/feature_counts/feature_counts_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=69587, disk_mib=66364, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:59:09 2024] -localrule feature_counts: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff - output: RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_Matrix_Optimal_Peak.mtx - log: RES_ATAC/09-CountMatrix/lanceOtron_narrow/logs/ATAC_counts.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=7630, disk_mb=69587, disk_mib=66364, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - featureCounts -T 1 -t peak -g gene_id -p -a RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff -o RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_Matrix_Optimal_Peak.mtx RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam 2> RES_ATAC/09-CountMatrix/lanceOtron_narrow/logs/ATAC_counts.out - -Activating singularity image epeak.sif -[Thu Sep 12 13:12:58 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out b/logs/slurm/feature_counts/feature_counts_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=H3K27ac.err b/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=H3K27ac.err deleted file mode 100644 index db186b0..0000000 --- a/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=H3K27ac.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10427, disk_mib=9944, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:12:20 2024] -localrule feature_counts: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.gff - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_Matrix_Optimal_Peak.mtx - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/H3K27ac_counts.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=H3K27ac - resources: mem_mb=9537, mem_mib=7630, disk_mb=10427, disk_mib=9944, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - featureCounts -T 1 -t peak -g gene_id -a /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.gff -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_Matrix_Optimal_Peak.mtx /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/H3K27ac_counts.out - -Activating singularity image epeak.sif -[Thu Sep 12 11:14:36 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=H3K27ac.out b/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=H3K27ac.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=Klf4.err b/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=Klf4.err deleted file mode 100644 index f7a5b30..0000000 --- a/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=Klf4.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=14904, disk_mib=14214, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:16:18 2024] -localrule feature_counts: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.gff - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_Matrix_Optimal_Peak.mtx - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/Klf4_counts.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=Klf4 - resources: mem_mb=9537, mem_mib=7630, disk_mb=14904, disk_mib=14214, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - featureCounts -T 1 -t peak -g gene_id -a /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.gff -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_Matrix_Optimal_Peak.mtx /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/Klf4_counts.out - -Activating singularity image epeak.sif -[Thu Sep 12 11:19:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=Klf4.out b/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=Klf4.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err b/logs/slurm/feature_counts/feature_counts_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err deleted file mode 100644 index a91aee6..0000000 --- a/logs/slurm/feature_counts/feature_counts_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=69587, disk_mib=66364, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:58:49 2024] -localrule feature_counts: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam, RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff - output: RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_Matrix_Optimal_Peak.mtx - log: RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/logs/ATAC_counts.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, MARK=ATAC - resources: mem_mb=9537, mem_mib=7630, disk_mb=69587, disk_mib=66364, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - featureCounts -T 1 -t peak -g gene_id -p -a RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff -o RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_Matrix_Optimal_Peak.mtx RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam 2> RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/logs/ATAC_counts.out - -Activating singularity image epeak.sif -[Thu Sep 12 12:13:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/feature_counts/feature_counts_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out b/logs/slurm/feature_counts/feature_counts_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.err deleted file mode 100644 index e06aeb2..0000000 --- a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=12025, disk_mib=11468, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:27:45 2024] -localrule genrich: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep1.out, RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep1.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/GENRICH_ATAC_D0_rep1.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1 - resources: mem_mb=19073, mem_mib=7630, disk_mb=12025, disk_mib=11468, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - # Sort by name the input file - samtools sort -n RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1.bam - - # Execute Genrich from it repository - ./workflow/scripts/Genrich-master/Genrich -t RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak_notsort -j > RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep1.out 2> RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep1.err - - # Rewrite the name peaks - awk -F' ' '{OFS=FS}{$4="genrich_narrow/ATAC_D0_rep1_" $4 ; print }' RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak_notsort > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak_temp - - # Sort the output - bedtools sort -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak_temp > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak - - rm RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak_temp - - -Activating singularity image epeak.sif -[bam_sort_core] merging from 15 files and 1 in-memory blocks... -[Thu Sep 12 12:15:12 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.out b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.err deleted file mode 100644 index ed5e4a6..0000000 --- a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=10754, disk_mib=10256, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:30:43 2024] -localrule genrich: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep2.out, RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep2.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/GENRICH_ATAC_D0_rep2.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2 - resources: mem_mb=19073, mem_mib=7630, disk_mb=10754, disk_mib=10256, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - # Sort by name the input file - samtools sort -n RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2.bam - - # Execute Genrich from it repository - ./workflow/scripts/Genrich-master/Genrich -t RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak_notsort -j > RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep2.out 2> RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep2.err - - # Rewrite the name peaks - awk -F' ' '{OFS=FS}{$4="genrich_narrow/ATAC_D0_rep2_" $4 ; print }' RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak_notsort > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak_temp - - # Sort the output - bedtools sort -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak_temp > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak - - rm RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak_temp - - -Activating singularity image epeak.sif -[bam_sort_core] merging from 9 files and 1 in-memory blocks... -[Thu Sep 12 11:10:54 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.out b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.err deleted file mode 100644 index 64a1bae..0000000 --- a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7630, disk_mb=9524, disk_mib=9083, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 07:47:48 2024] -localrule genrich: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep3.out, RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep3.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/GENRICH_ATAC_D0_rep3.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3 - resources: mem_mb=19073, mem_mib=7630, disk_mb=9524, disk_mib=9083, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - # Sort by name the input file - samtools sort -n RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3.bam - - # Execute Genrich from it repository - ./workflow/scripts/Genrich-master/Genrich -t RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak_notsort -j > RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep3.out 2> RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D0_rep3.err - - # Rewrite the name peaks - awk -F' ' '{OFS=FS}{$4="genrich_narrow/ATAC_D0_rep3_" $4 ; print }' RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak_notsort > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak_temp - - # Sort the output - bedtools sort -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak_temp > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak - - rm RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak_temp - - -Activating singularity image epeak.sif -[bam_sort_core] merging from 5 files and 1 in-memory blocks... -[Thu Sep 12 08:24:03 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.out b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.err deleted file mode 100644 index 8df566d..0000000 --- a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=5065, disk_mb=5310, disk_mib=5065, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:52:51 2024] -localrule genrich: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep1.out, RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep1.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/GENRICH_ATAC_D6F_rep1.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1 - resources: mem_mb=19073, mem_mib=5065, disk_mb=5310, disk_mib=5065, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - # Sort by name the input file - samtools sort -n RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1.bam - - # Execute Genrich from it repository - ./workflow/scripts/Genrich-master/Genrich -t RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak_notsort -j > RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep1.out 2> RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep1.err - - # Rewrite the name peaks - awk -F' ' '{OFS=FS}{$4="genrich_narrow/ATAC_D6F_rep1_" $4 ; print }' RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak_notsort > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak_temp - - # Sort the output - bedtools sort -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak_temp > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak - - rm RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak_temp - - -Activating singularity image epeak.sif -[bam_sort_core] merging from 19 files and 1 in-memory blocks... -[Thu Sep 12 01:09:29 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.out b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.err deleted file mode 100644 index ca8d9ce..0000000 --- a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=5250, disk_mb=5504, disk_mib=5250, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:54:49 2024] -localrule genrich: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep2.out, RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep2.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/GENRICH_ATAC_D6F_rep2.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2 - resources: mem_mb=19073, mem_mib=5250, disk_mb=5504, disk_mib=5250, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - # Sort by name the input file - samtools sort -n RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2.bam - - # Execute Genrich from it repository - ./workflow/scripts/Genrich-master/Genrich -t RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak_notsort -j > RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep2.out 2> RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep2.err - - # Rewrite the name peaks - awk -F' ' '{OFS=FS}{$4="genrich_narrow/ATAC_D6F_rep2_" $4 ; print }' RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak_notsort > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak_temp - - # Sort the output - bedtools sort -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak_temp > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak - - rm RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak_temp - - -Activating singularity image epeak.sif -[bam_sort_core] merging from 20 files and 1 in-memory blocks... -[Thu Sep 12 00:12:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.out b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.err deleted file mode 100644 index 364de0d..0000000 --- a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=6182, disk_mb=6482, disk_mib=6182, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 02:11:50 2024] -localrule genrich: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep3.out, RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep3.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/GENRICH_ATAC_D6F_rep3.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3 - resources: mem_mb=19073, mem_mib=6182, disk_mb=6482, disk_mib=6182, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - # Sort by name the input file - samtools sort -n RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3.bam - - # Execute Genrich from it repository - ./workflow/scripts/Genrich-master/Genrich -t RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak_notsort -j > RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep3.out 2> RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6F_rep3.err - - # Rewrite the name peaks - awk -F' ' '{OFS=FS}{$4="genrich_narrow/ATAC_D6F_rep3_" $4 ; print }' RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak_notsort > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak_temp - - # Sort the output - bedtools sort -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak_temp > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak - - rm RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak_temp - - -Activating singularity image epeak.sif -[bam_sort_core] merging from 24 files and 1 in-memory blocks... -[Thu Sep 12 02:32:21 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.out b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.err deleted file mode 100644 index bbc8009..0000000 --- a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=5709, disk_mb=5986, disk_mib=5709, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:25:43 2024] -localrule genrich: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep1.out, RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep1.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/GENRICH_ATAC_D6_rep1.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1 - resources: mem_mb=19073, mem_mib=5709, disk_mb=5986, disk_mib=5709, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - # Sort by name the input file - samtools sort -n RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1.bam - - # Execute Genrich from it repository - ./workflow/scripts/Genrich-master/Genrich -t RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak_notsort -j > RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep1.out 2> RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep1.err - - # Rewrite the name peaks - awk -F' ' '{OFS=FS}{$4="genrich_narrow/ATAC_D6_rep1_" $4 ; print }' RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak_notsort > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak_temp - - # Sort the output - bedtools sort -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak_temp > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak - - rm RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak_temp - - -Activating singularity image epeak.sif -[bam_sort_core] merging from 22 files and 1 in-memory blocks... -[Thu Sep 12 00:44:30 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.out b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.err deleted file mode 100644 index 8cbcd8e..0000000 --- a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=7497, disk_mb=7861, disk_mib=7497, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 05:16:44 2024] -localrule genrich: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep2.out, RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep2.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/GENRICH_ATAC_D6_rep2.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2 - resources: mem_mb=19073, mem_mib=7497, disk_mb=7861, disk_mib=7497, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - # Sort by name the input file - samtools sort -n RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2.bam - - # Execute Genrich from it repository - ./workflow/scripts/Genrich-master/Genrich -t RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak_notsort -j > RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep2.out 2> RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep2.err - - # Rewrite the name peaks - awk -F' ' '{OFS=FS}{$4="genrich_narrow/ATAC_D6_rep2_" $4 ; print }' RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak_notsort > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak_temp - - # Sort the output - bedtools sort -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak_temp > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak - - rm RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak_temp - - -Activating singularity image epeak.sif -[bam_sort_core] merging from 29 files and 1 in-memory blocks... -[Thu Sep 12 05:41:33 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.out b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.err deleted file mode 100644 index 3d55816..0000000 --- a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.err +++ /dev/null @@ -1,47 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=5850, disk_mb=6134, disk_mib=5850, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:17:44 2024] -localrule genrich: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep3.out, RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep3.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/GENRICH_ATAC_D6_rep3.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3 - resources: mem_mb=19073, mem_mib=5850, disk_mb=6134, disk_mib=5850, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - # Sort by name the input file - samtools sort -n RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3.bam - - # Execute Genrich from it repository - ./workflow/scripts/Genrich-master/Genrich -t RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3.bam -o RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak_notsort -j > RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep3.out 2> RES_ATAC/06-PeakCalling/genrich_narrow/log/ATAC_D6_rep3.err - - # Rewrite the name peaks - awk -F' ' '{OFS=FS}{$4="genrich_narrow/ATAC_D6_rep3_" $4 ; print }' RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak_notsort > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak_temp - - # Sort the output - bedtools sort -i RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak_temp > RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak - - rm RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak_temp - - -Activating singularity image epeak.sif -[bam_sort_core] merging from 23 files and 1 in-memory blocks... -[Thu Sep 12 10:35:55 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.out b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/igv_session/igv_session_unique.err b/logs/slurm/igv_session/igv_session_unique.err deleted file mode 100644 index e25a489..0000000 --- a/logs/slurm/igv_session/igv_session_unique.err +++ /dev/null @@ -1,27 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5576, disk_mb=5846, disk_mib=5576, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:15:50 2024] -localrule igv_session: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep2_mm10_coverage.bw, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shCtrl_Rep1_mm10_coverage.bw, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep1_mm10_coverage.bw, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/H3K27ac_shUbc9_Rep2_mm10_coverage.bw, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep2_mm10_coverage.bw, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shCtrl_Rep1_mm10_coverage.bw, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep1_mm10_coverage.bw, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/Klf4_shUbc9_Rep2_mm10_coverage.bw, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_IA.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_IA.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_IA.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/igv_session.xml - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/12-IGV/logs/igv_session.out - jobid: 0 - reason: Forced execution - resources: mem_mb=9537, mem_mib=5576, disk_mb=5846, disk_mib=5576, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -[Thu Sep 12 11:15:53 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/igv_session/igv_session_unique.out b/logs/slurm/igv_session/igv_session_unique.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=genrich.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=genrich.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err deleted file mode 100644 index dd81abb..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=genrich.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 11:33:58 2024] -localrule individualPeakAnnotation: - input: RES_ATAC2/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/ATAC_D0_rep3_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/logs/ATAC_D0_rep3_narrow_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, SAMPLE=ATAC_D0_rep3, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - fi - -Activating singularity image epeak.sif -[Wed Sep 4 11:34:14 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: RES_ATAC2/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/ATAC_D0_rep3_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/logs/ATAC_D0_rep3_narrow_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/genrich_narrow/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - fi - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=genrich.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=genrich.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.err deleted file mode 100644 index 74e8b97..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 11:34:02 2024] -localrule individualPeakAnnotation: - input: RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep1_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep1_narrow_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, SAMPLE=ATAC_D0_rep1, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep1_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep1_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep1_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep1_narrow_peaks.out 2>&1 - fi - -Activating singularity image epeak.sif -[Wed Sep 4 11:34:28 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep1_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep1_narrow_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep1_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep1_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep1_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep1_narrow_peaks.out 2>&1 - fi - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.err deleted file mode 100644 index 9113df2..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 11:34:02 2024] -localrule individualPeakAnnotation: - input: RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep2_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep2_narrow_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, SAMPLE=ATAC_D0_rep2, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep2_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep2_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep2_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep2_narrow_peaks.out 2>&1 - fi - -Activating singularity image epeak.sif -[Wed Sep 4 11:34:28 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep2_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep2_narrow_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep2_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep2_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep2_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep2_narrow_peaks.out 2>&1 - fi - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err deleted file mode 100644 index be16ce3..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 11:34:02 2024] -localrule individualPeakAnnotation: - input: RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep3_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep3_narrow_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, SAMPLE=ATAC_D0_rep3, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - fi - -Activating singularity image epeak.sif -[Wed Sep 4 11:34:28 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep3_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep3_narrow_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/lanceOtron_narrow/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - fi - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.err deleted file mode 100644 index 9a78006..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:11:06 2024] -localrule individualPeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep1_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep1_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=H3K27ac_shCtrl, CASE=Rep1 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep1_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep1_peaks.out 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 23:11:26 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep1_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep1_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep1_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep1_peaks.out 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.err deleted file mode 100644 index fa8861b..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:11:09 2024] -localrule individualPeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep2_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep2_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=H3K27ac_shCtrl, CASE=Rep2 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep2_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep2_peaks.out 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 23:11:31 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep2_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep2_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep2_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_Rep2_peaks.out 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.err deleted file mode 100644 index f7dc4d7..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:19 2024] -localrule individualPeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep1_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep1_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=H3K27ac_shUbc9, CASE=Rep1 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep1_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep1_peaks.out 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:39 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep1_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep1_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep1_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep1_peaks.out 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.err deleted file mode 100644 index 9abcb5c..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:22 2024] -localrule individualPeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep2_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep2_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=H3K27ac_shUbc9, CASE=Rep2 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep2_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep2_peaks.out 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:48 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep2_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep2_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep2_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_Rep2_peaks.out 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.err deleted file mode 100644 index bc3c70f..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:11:12 2024] -localrule individualPeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep1_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep1_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=Klf4_shCtrl, CASE=Rep1 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep1_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep1_peaks.out 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 23:11:33 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep1_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep1_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep1_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep1_peaks.out 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.err deleted file mode 100644 index 482d476..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:19 2024] -localrule individualPeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep2_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep2_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=Klf4_shCtrl, CASE=Rep2 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep2_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep2_peaks.out 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:41 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep2_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep2_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep2_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shCtrl_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_Rep2_peaks.out 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.err deleted file mode 100644 index 7517e54..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:23 2024] -localrule individualPeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep1_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep1_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=Klf4_shUbc9, CASE=Rep1 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep1_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep1_peaks.out 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:41 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep1_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep1_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep1_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep1_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep1_peaks.out 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.err deleted file mode 100644 index 86a3ab3..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:22 2024] -localrule individualPeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep2_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep2_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=Klf4_shUbc9, CASE=Rep2 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep2_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep2_peaks.out 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:50 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep2_peaks.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep2_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep2_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/Klf4_shUbc9_Rep2_peaks.txt >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_Rep2_peaks.out 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.err deleted file mode 100644 index 7532d34..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 11:34:00 2024] -localrule individualPeakAnnotation: - input: RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep1_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep1_narrow_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, SAMPLE=ATAC_D0_rep1, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep1_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep1_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep1_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep1_narrow_peaks.out 2>&1 - fi - -Activating singularity image epeak.sif -[Wed Sep 4 11:34:26 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep1_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep1_narrow_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep1_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep1_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep1_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep1_narrow_peaks.out 2>&1 - fi - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.err deleted file mode 100644 index 9ccb36f..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 11:33:58 2024] -localrule individualPeakAnnotation: - input: RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep2_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep2_narrow_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, SAMPLE=ATAC_D0_rep2, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep2_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep2_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep2_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep2_narrow_peaks.out 2>&1 - fi - -Activating singularity image epeak.sif -[Wed Sep 4 11:34:23 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep2_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep2_narrow_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep2_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep2_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep2_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep2_narrow_peaks.out 2>&1 - fi - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.err b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.err deleted file mode 100644 index bdd8e77..0000000 --- a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.err +++ /dev/null @@ -1,55 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 11:34:00 2024] -localrule individualPeakAnnotation: - input: RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep3_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep3_narrow_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, SAMPLE=ATAC_D0_rep3, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - fi - -Activating singularity image epeak.sif -[Wed Sep 4 11:34:27 2024] -Error in rule individualPeakAnnotation: - jobid: 0 - input: RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak - output: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep3_narrow_peaks.txt - log: RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep3_narrow_peaks.out (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ]; then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt RES_ATAC2/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/ATAC_D0_rep3_narrow_peaks.txt >RES_ATAC2/06-PeakCalling/Annotation_peaks/macs3_CallPeak_noModel/logs/ATAC_D0_rep3_narrow_peaks.out 2>&1 - fi - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.out b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.err b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.err deleted file mode 100644 index 1685313..0000000 --- a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12025, disk_mib=11468, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:27:45 2024] -localrule insert_size_metrics: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep1_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep1_hg38_fragmentSizeDistribution.pdf - log: RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep1_hg38_fragment_size.out, RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep1_hg38_fragment_size.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=12025, disk_mib=11468, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard CollectInsertSizeMetrics I=RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep1_hg38_fragmentSizeDistribution.txt H=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep1_hg38_fragmentSizeDistribution.pdf > RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep1_hg38_fragment_size.out 2> RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep1_hg38_fragment_size.err - - -Activating singularity image epeak.sif -[Thu Sep 12 11:31:15 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.out b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.err b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.err deleted file mode 100644 index d4f3c9b..0000000 --- a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10754, disk_mib=10256, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:30:45 2024] -localrule insert_size_metrics: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep2_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep2_hg38_fragmentSizeDistribution.pdf - log: RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep2_hg38_fragment_size.out, RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep2_hg38_fragment_size.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=10754, disk_mib=10256, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard CollectInsertSizeMetrics I=RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep2_hg38_fragmentSizeDistribution.txt H=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep2_hg38_fragmentSizeDistribution.pdf > RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep2_hg38_fragment_size.out 2> RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep2_hg38_fragment_size.err - - -Activating singularity image epeak.sif -[Thu Sep 12 10:33:37 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.out b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.err b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.err deleted file mode 100644 index a6d2c01..0000000 --- a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9524, disk_mib=9083, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 07:47:48 2024] -localrule insert_size_metrics: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep3_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep3_hg38_fragmentSizeDistribution.pdf - log: RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep3_hg38_fragment_size.out, RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep3_hg38_fragment_size.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=9524, disk_mib=9083, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard CollectInsertSizeMetrics I=RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep3_hg38_fragmentSizeDistribution.txt H=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep3_hg38_fragmentSizeDistribution.pdf > RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep3_hg38_fragment_size.out 2> RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D0_rep3_hg38_fragment_size.err - - -Activating singularity image epeak.sif -[Thu Sep 12 07:50:27 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.out b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.err b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.err deleted file mode 100644 index 09d928e..0000000 --- a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5065, disk_mb=5310, disk_mib=5065, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:52:51 2024] -localrule insert_size_metrics: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep1_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep1_hg38_fragmentSizeDistribution.pdf - log: RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep1_hg38_fragment_size.out, RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep1_hg38_fragment_size.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=5065, disk_mb=5310, disk_mib=5065, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard CollectInsertSizeMetrics I=RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep1_hg38_fragmentSizeDistribution.txt H=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep1_hg38_fragmentSizeDistribution.pdf > RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep1_hg38_fragment_size.out 2> RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep1_hg38_fragment_size.err - - -Activating singularity image epeak.sif -[Thu Sep 12 00:54:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.out b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.err b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.err deleted file mode 100644 index a0fce25..0000000 --- a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5250, disk_mb=5504, disk_mib=5250, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:54:49 2024] -localrule insert_size_metrics: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep2_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep2_hg38_fragmentSizeDistribution.pdf - log: RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep2_hg38_fragment_size.out, RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep2_hg38_fragment_size.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=5250, disk_mb=5504, disk_mib=5250, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard CollectInsertSizeMetrics I=RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep2_hg38_fragmentSizeDistribution.txt H=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep2_hg38_fragmentSizeDistribution.pdf > RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep2_hg38_fragment_size.out 2> RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep2_hg38_fragment_size.err - - -Activating singularity image epeak.sif -[Wed Sep 11 23:56:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.out b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.err b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.err deleted file mode 100644 index 4f49d7f..0000000 --- a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6182, disk_mb=6482, disk_mib=6182, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 02:11:50 2024] -localrule insert_size_metrics: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep3_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep3_hg38_fragmentSizeDistribution.pdf - log: RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep3_hg38_fragment_size.out, RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep3_hg38_fragment_size.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3, REF=hg38 - resources: mem_mb=9537, mem_mib=6182, disk_mb=6482, disk_mib=6182, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard CollectInsertSizeMetrics I=RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep3_hg38_fragmentSizeDistribution.txt H=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep3_hg38_fragmentSizeDistribution.pdf > RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep3_hg38_fragment_size.out 2> RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6F_rep3_hg38_fragment_size.err - - -Activating singularity image epeak.sif -[Thu Sep 12 02:13:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.out b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.err b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.err deleted file mode 100644 index e8dc4dd..0000000 --- a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5709, disk_mb=5986, disk_mib=5709, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:25:43 2024] -localrule insert_size_metrics: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep1_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep1_hg38_fragmentSizeDistribution.pdf - log: RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep1_hg38_fragment_size.out, RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep1_hg38_fragment_size.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=5709, disk_mb=5986, disk_mib=5709, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard CollectInsertSizeMetrics I=RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep1_hg38_fragmentSizeDistribution.txt H=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep1_hg38_fragmentSizeDistribution.pdf > RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep1_hg38_fragment_size.out 2> RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep1_hg38_fragment_size.err - - -Activating singularity image epeak.sif -[Thu Sep 12 00:27:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.out b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.err b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.err deleted file mode 100644 index a67ea7d..0000000 --- a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7497, disk_mb=7861, disk_mib=7497, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 05:16:44 2024] -localrule insert_size_metrics: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep2_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep2_hg38_fragmentSizeDistribution.pdf - log: RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep2_hg38_fragment_size.out, RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep2_hg38_fragment_size.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=7497, disk_mb=7861, disk_mib=7497, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard CollectInsertSizeMetrics I=RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep2_hg38_fragmentSizeDistribution.txt H=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep2_hg38_fragmentSizeDistribution.pdf > RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep2_hg38_fragment_size.out 2> RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep2_hg38_fragment_size.err - - -Activating singularity image epeak.sif -[Thu Sep 12 05:18:54 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.out b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.err b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.err deleted file mode 100644 index 2ee80e2..0000000 --- a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.err +++ /dev/null @@ -1,31 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5850, disk_mb=6134, disk_mib=5850, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:17:44 2024] -localrule insert_size_metrics: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep3_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep3_hg38_fragmentSizeDistribution.pdf - log: RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep3_hg38_fragment_size.out, RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep3_hg38_fragment_size.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3, REF=hg38 - resources: mem_mb=9537, mem_mib=5850, disk_mb=6134, disk_mib=5850, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - picard CollectInsertSizeMetrics I=RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam O=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep3_hg38_fragmentSizeDistribution.txt H=RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep3_hg38_fragmentSizeDistribution.pdf > RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep3_hg38_fragment_size.out 2> RES_ATAC/05-QC/FragmentSizeDistribution/logs/ATAC_D6_rep3_hg38_fragment_size.err - - -Activating singularity image epeak.sif -[Thu Sep 12 10:19:25 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.out b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.err b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.err deleted file mode 100644 index c8c73a3..0000000 --- a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:10:06 2024] -localrule intersectionApproach: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shCtrl_IA_peaks.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=H3K27ac_shCtrl - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - bed_files_list=`echo /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak | sed 's/ /,/g'` - python3 workflow/scripts/intersection_approach_filtering.py --bed-files-list=$bed_files_list --nb-min-replicates=2 --min-peak-length=0 --min-percentage-overlap=0.8 --output-file=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed 1>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shCtrl_IA_peaks.o 2>&1 - - if [ ! -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed ] ;then - echo "Error: file (/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed) is empty... No common peaks are found for this mark" 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shCtrl_IA_peaks.o - exit 5 - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:10:27 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.out b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.err b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.err deleted file mode 100644 index 195eeaf..0000000 --- a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:10:39 2024] -localrule intersectionApproach: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_IA.bed - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shUbc9_IA_peaks.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=H3K27ac_shUbc9 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - bed_files_list=`echo /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak | sed 's/ /,/g'` - python3 workflow/scripts/intersection_approach_filtering.py --bed-files-list=$bed_files_list --nb-min-replicates=2 --min-peak-length=0 --min-percentage-overlap=0.8 --output-file=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_IA.bed 1>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shUbc9_IA_peaks.o 2>&1 - - if [ ! -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_IA.bed ] ;then - echo "Error: file (/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_IA.bed) is empty... No common peaks are found for this mark" 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shUbc9_IA_peaks.o - exit 5 - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:10:59 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.out b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.err b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.err deleted file mode 100644 index f6850a6..0000000 --- a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:10:42 2024] -localrule intersectionApproach: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_IA.bed - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shCtrl_IA_peaks.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=Klf4_shCtrl - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - bed_files_list=`echo /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak | sed 's/ /,/g'` - python3 workflow/scripts/intersection_approach_filtering.py --bed-files-list=$bed_files_list --nb-min-replicates=2 --min-peak-length=0 --min-percentage-overlap=0.8 --output-file=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_IA.bed 1>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shCtrl_IA_peaks.o 2>&1 - - if [ ! -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_IA.bed ] ;then - echo "Error: file (/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_IA.bed) is empty... No common peaks are found for this mark" 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shCtrl_IA_peaks.o - exit 5 - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.out b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.err b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.err deleted file mode 100644 index 0506951..0000000 --- a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.err +++ /dev/null @@ -1,39 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:14:48 2024] -localrule intersectionApproach: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_IA.bed - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shUbc9_IA_peaks.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=Klf4_shUbc9 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - bed_files_list=`echo /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak | sed 's/ /,/g'` - python3 workflow/scripts/intersection_approach_filtering.py --bed-files-list=$bed_files_list --nb-min-replicates=2 --min-peak-length=0 --min-percentage-overlap=0.8 --output-file=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_IA.bed 1>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shUbc9_IA_peaks.o 2>&1 - - if [ ! -s /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_IA.bed ] ;then - echo "Error: file (/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_IA.bed) is empty... No common peaks are found for this mark" 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shUbc9_IA_peaks.o - exit 5 - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:15:05 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.out b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.err deleted file mode 100644 index c3b6fa6..0000000 --- a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:49:44 2024] -localrule lanceotron: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep1_dedup_sort.bw - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep1_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep1_dedup_sort.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/LANCEOTRON_ATAC_D0_rep1.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - lanceotron callPeaks RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep1_dedup_sort.bw -f RES_ATAC/06-PeakCalling/lanceOtron_narrow/ -w 500 -t 5 > RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep1_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep1_dedup_sort.err - - # May have to recheck the column to take - tail -n +2 RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_dedup_sort_L-tron.bed | awk '{print$1,$2,$3,"lanceOtron_narrow/ATAC_D0_rep1_peaks_"NR,int($6*1000),".",$6,$9,$10,int($7)}' OFS=' ' | bedtools sort -i > RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak - - -Activating singularity image epeak.sif -[Thu Sep 12 12:10:31 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.out b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.err deleted file mode 100644 index 3d6188e..0000000 --- a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:51:10 2024] -localrule lanceotron: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep2_dedup_sort.bw - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep2_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep2_dedup_sort.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/LANCEOTRON_ATAC_D0_rep2.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - lanceotron callPeaks RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep2_dedup_sort.bw -f RES_ATAC/06-PeakCalling/lanceOtron_narrow/ -w 500 -t 5 > RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep2_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep2_dedup_sort.err - - # May have to recheck the column to take - tail -n +2 RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_dedup_sort_L-tron.bed | awk '{print$1,$2,$3,"lanceOtron_narrow/ATAC_D0_rep2_peaks_"NR,int($6*1000),".",$6,$9,$10,int($7)}' OFS=' ' | bedtools sort -i > RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak - - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:31 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.out b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.err deleted file mode 100644 index 7c5856a..0000000 --- a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 08:05:47 2024] -localrule lanceotron: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep3_dedup_sort.bw - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep3_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep3_dedup_sort.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/LANCEOTRON_ATAC_D0_rep3.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - lanceotron callPeaks RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep3_dedup_sort.bw -f RES_ATAC/06-PeakCalling/lanceOtron_narrow/ -w 500 -t 5 > RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep3_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D0_rep3_dedup_sort.err - - # May have to recheck the column to take - tail -n +2 RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_dedup_sort_L-tron.bed | awk '{print$1,$2,$3,"lanceOtron_narrow/ATAC_D0_rep3_peaks_"NR,int($6*1000),".",$6,$9,$10,int($7)}' OFS=' ' | bedtools sort -i > RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak - - -Activating singularity image epeak.sif -[Thu Sep 12 08:25:34 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.out b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.err deleted file mode 100644 index 2e86341..0000000 --- a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 01:03:47 2024] -localrule lanceotron: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep1_dedup_sort.bw - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep1_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep1_dedup_sort.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/LANCEOTRON_ATAC_D6F_rep1.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - lanceotron callPeaks RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep1_dedup_sort.bw -f RES_ATAC/06-PeakCalling/lanceOtron_narrow/ -w 500 -t 5 > RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep1_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep1_dedup_sort.err - - # May have to recheck the column to take - tail -n +2 RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_dedup_sort_L-tron.bed | awk '{print$1,$2,$3,"lanceOtron_narrow/ATAC_D6F_rep1_peaks_"NR,int($6*1000),".",$6,$9,$10,int($7)}' OFS=' ' | bedtools sort -i > RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak - - -Activating singularity image epeak.sif -[Thu Sep 12 01:24:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.out b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.err deleted file mode 100644 index 34074f4..0000000 --- a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:05:55 2024] -localrule lanceotron: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep2_dedup_sort.bw - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep2_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep2_dedup_sort.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/LANCEOTRON_ATAC_D6F_rep2.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - lanceotron callPeaks RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep2_dedup_sort.bw -f RES_ATAC/06-PeakCalling/lanceOtron_narrow/ -w 500 -t 5 > RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep2_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep2_dedup_sort.err - - # May have to recheck the column to take - tail -n +2 RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_dedup_sort_L-tron.bed | awk '{print$1,$2,$3,"lanceOtron_narrow/ATAC_D6F_rep2_peaks_"NR,int($6*1000),".",$6,$9,$10,int($7)}' OFS=' ' | bedtools sort -i > RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak - - -Activating singularity image epeak.sif -[Thu Sep 12 00:28:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.out b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.err deleted file mode 100644 index d0bb8b3..0000000 --- a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 02:24:49 2024] -localrule lanceotron: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep3_dedup_sort.bw - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep3_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep3_dedup_sort.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/LANCEOTRON_ATAC_D6F_rep3.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - lanceotron callPeaks RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep3_dedup_sort.bw -f RES_ATAC/06-PeakCalling/lanceOtron_narrow/ -w 500 -t 5 > RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep3_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6F_rep3_dedup_sort.err - - # May have to recheck the column to take - tail -n +2 RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_dedup_sort_L-tron.bed | awk '{print$1,$2,$3,"lanceOtron_narrow/ATAC_D6F_rep3_peaks_"NR,int($6*1000),".",$6,$9,$10,int($7)}' OFS=' ' | bedtools sort -i > RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak - - -Activating singularity image epeak.sif -[Thu Sep 12 02:46:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.out b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.err deleted file mode 100644 index 28770ea..0000000 --- a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:37:38 2024] -localrule lanceotron: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep1_dedup_sort.bw - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep1_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep1_dedup_sort.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/LANCEOTRON_ATAC_D6_rep1.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - lanceotron callPeaks RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep1_dedup_sort.bw -f RES_ATAC/06-PeakCalling/lanceOtron_narrow/ -w 500 -t 5 > RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep1_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep1_dedup_sort.err - - # May have to recheck the column to take - tail -n +2 RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_dedup_sort_L-tron.bed | awk '{print$1,$2,$3,"lanceOtron_narrow/ATAC_D6_rep1_peaks_"NR,int($6*1000),".",$6,$9,$10,int($7)}' OFS=' ' | bedtools sort -i > RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak - - -Activating singularity image epeak.sif -[Thu Sep 12 00:59:37 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.out b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.err deleted file mode 100644 index e628c81..0000000 --- a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 05:31:43 2024] -localrule lanceotron: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep2_dedup_sort.bw - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep2_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep2_dedup_sort.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/LANCEOTRON_ATAC_D6_rep2.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - lanceotron callPeaks RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep2_dedup_sort.bw -f RES_ATAC/06-PeakCalling/lanceOtron_narrow/ -w 500 -t 5 > RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep2_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep2_dedup_sort.err - - # May have to recheck the column to take - tail -n +2 RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_dedup_sort_L-tron.bed | awk '{print$1,$2,$3,"lanceOtron_narrow/ATAC_D6_rep2_peaks_"NR,int($6*1000),".",$6,$9,$10,int($7)}' OFS=' ' | bedtools sort -i > RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak - - -Activating singularity image epeak.sif -[Thu Sep 12 05:51:58 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.out b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.err deleted file mode 100644 index af39fad..0000000 --- a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:29:52 2024] -localrule lanceotron: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep3_dedup_sort.bw - output: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep3_dedup_sort.out, RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep3_dedup_sort.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/LANCEOTRON_ATAC_D6_rep3.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3 - resources: mem_mb=28610, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=30G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - lanceotron callPeaks RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep3_dedup_sort.bw -f RES_ATAC/06-PeakCalling/lanceOtron_narrow/ -w 500 -t 5 > RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep3_dedup_sort.out 2> RES_ATAC/06-PeakCalling/lanceOtron_narrow/logs/ATAC_D6_rep3_dedup_sort.err - - # May have to recheck the column to take - tail -n +2 RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_dedup_sort_L-tron.bed | awk '{print$1,$2,$3,"lanceOtron_narrow/ATAC_D6_rep3_peaks_"NR,int($6*1000),".",$6,$9,$10,int($7)}' OFS=' ' | bedtools sort -i > RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak - - -Activating singularity image epeak.sif -[Thu Sep 12 10:43:45 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.out b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.err deleted file mode 100644 index bdabfc3..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7019, disk_mb=7359, disk_mib=7019, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_PPR1 - resources: mem_mb=9537, mem_mib=7019, disk_mb=7359, disk_mib=7019, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR1.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:09:55 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.err deleted file mode 100644 index 16c96d8..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7019, disk_mb=7359, disk_mib=7019, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:04 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_PPR2 - resources: mem_mb=9537, mem_mib=7019, disk_mb=7359, disk_mib=7019, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPR2.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:09:47 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.err deleted file mode 100644 index e9221b8..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12054, disk_mib=11496, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:06 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPRPool_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_PPRPool - resources: mem_mb=9537, mem_mib=7630, disk_mb=12054, disk_mib=11496, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_PPRPool.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:11:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.err deleted file mode 100644 index b56ddc2..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6985, disk_mb=7324, disk_mib=6985, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:06 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=6985, disk_mb=7324, disk_mib=6985, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep1.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:09:50 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.err deleted file mode 100644 index 12306c3..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6679, disk_mb=7003, disk_mib=6679, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:06 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=6679, disk_mb=7003, disk_mib=6679, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_Rep2.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:09:44 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.err deleted file mode 100644 index 432e164..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4581, disk_mb=4803, disk_mib=4581, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:06 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_SPR1.1 - resources: mem_mb=9537, mem_mib=4581, disk_mb=4803, disk_mib=4581, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.1.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:09:02 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.err deleted file mode 100644 index 41cec46..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4581, disk_mb=4803, disk_mib=4581, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_SPR1.2 - resources: mem_mb=9537, mem_mib=4581, disk_mb=4803, disk_mib=4581, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR1.2.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:09:00 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.err deleted file mode 100644 index facfb82..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4415, disk_mb=4629, disk_mib=4415, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:06 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_SPR2.1 - resources: mem_mb=9537, mem_mib=4415, disk_mb=4629, disk_mib=4415, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.1.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:08:57 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.err deleted file mode 100644 index 769f2a1..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4415, disk_mb=4629, disk_mib=4415, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_SPR2.2 - resources: mem_mb=9537, mem_mib=4415, disk_mb=4629, disk_mib=4415, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shCtrl_SPR2.2.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:08:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.err deleted file mode 100644 index 1d62d31..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7544, disk_mb=7910, disk_mib=7544, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_PPR1 - resources: mem_mb=9537, mem_mib=7544, disk_mb=7910, disk_mib=7544, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR1.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:10:01 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.err deleted file mode 100644 index 3c2bd18..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7544, disk_mb=7910, disk_mib=7544, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_PPR2 - resources: mem_mb=9537, mem_mib=7544, disk_mb=7910, disk_mib=7544, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPR2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:59 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.err deleted file mode 100644 index f33ac7e..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12603, disk_mib=12020, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPRPool_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_PPRPool - resources: mem_mb=9537, mem_mib=7630, disk_mb=12603, disk_mib=12020, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_PPRPool.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:40 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.err deleted file mode 100644 index cb433b7..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7589, disk_mb=7957, disk_mib=7589, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=7589, disk_mb=7957, disk_mib=7589, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep1.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:10:01 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.err deleted file mode 100644 index 6a60f0b..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7123, disk_mb=7469, disk_mib=7123, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=7123, disk_mb=7469, disk_mib=7123, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_Rep2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.err deleted file mode 100644 index d132c8c..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5150, disk_mb=5400, disk_mib=5150, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_SPR1.1 - resources: mem_mb=9537, mem_mib=5150, disk_mb=5400, disk_mib=5150, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.1.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:09 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.err deleted file mode 100644 index 6f11b4b..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5150, disk_mb=5400, disk_mib=5150, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_SPR1.2 - resources: mem_mb=9537, mem_mib=5150, disk_mb=5400, disk_mib=5150, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR1.2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:06 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.err deleted file mode 100644 index 3c5fedc..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4895, disk_mb=5132, disk_mib=4895, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_SPR2.1 - resources: mem_mb=9537, mem_mib=4895, disk_mb=5132, disk_mib=4895, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.1.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:08:34 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.err deleted file mode 100644 index af5fc2c..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4895, disk_mb=5132, disk_mib=4895, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_SPR2.2 - resources: mem_mb=9537, mem_mib=4895, disk_mb=5132, disk_mib=4895, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/H3K27ac_shUbc9_SPR2.2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:08:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.out b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.err deleted file mode 100644 index 232691e..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9004, disk_mib=8587, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_PPR1 - resources: mem_mb=9537, mem_mib=7630, disk_mb=9004, disk_mib=8587, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR1.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:10:36 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.err deleted file mode 100644 index ea9d442..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9841, disk_mib=9386, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:16 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_PPR2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=9841, disk_mib=9386, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPR2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.err deleted file mode 100644 index 5c867f2..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=15795, disk_mib=15064, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:16 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPRPool_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_PPRPool - resources: mem_mb=9537, mem_mib=7630, disk_mb=15795, disk_mib=15064, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_PPRPool.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:13:29 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.err deleted file mode 100644 index 89922c8..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9114, disk_mib=8692, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=7630, disk_mb=9114, disk_mib=8692, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep1.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:10:42 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.err deleted file mode 100644 index 4383bd4..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9150, disk_mib=8727, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:02 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=9150, disk_mib=8727, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_Rep2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.err deleted file mode 100644 index f2bcabc..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5498, disk_mb=5765, disk_mib=5498, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_SPR1.1 - resources: mem_mb=9537, mem_mib=5498, disk_mb=5765, disk_mib=5498, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.1.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:09:21 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.err deleted file mode 100644 index 2b15b01..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5499, disk_mb=5766, disk_mib=5499, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_SPR1.2 - resources: mem_mb=9537, mem_mib=5499, disk_mb=5766, disk_mib=5499, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR1.2.err - fi - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:09:09 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.err deleted file mode 100644 index b13d466..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5896, disk_mb=6182, disk_mib=5896, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:04 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_SPR2.1 - resources: mem_mb=9537, mem_mib=5896, disk_mb=6182, disk_mib=5896, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.1.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:14 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.err deleted file mode 100644 index 01c8c53..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5896, disk_mb=6182, disk_mib=5896, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:04 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_SPR2.2 - resources: mem_mb=9537, mem_mib=5896, disk_mb=6182, disk_mib=5896, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shCtrl_SPR2.2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:11 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.err deleted file mode 100644 index 52c0d4b..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=11017, disk_mib=10507, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_PPR1 - resources: mem_mb=9537, mem_mib=7630, disk_mb=11017, disk_mib=10507, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR1.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:10:41 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.err deleted file mode 100644 index 3e9bb50..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=11713, disk_mib=11171, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:05:39 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_PPR2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=11713, disk_mib=11171, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPR2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:13:21 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.err deleted file mode 100644 index c36ab54..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=18155, disk_mib=17314, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPRPool_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_PPRPool - resources: mem_mb=9537, mem_mib=7630, disk_mb=18155, disk_mib=17314, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPRPool -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_PPRPool.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:13:30 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.err deleted file mode 100644 index a151487..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9786, disk_mib=9333, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=7630, disk_mb=9786, disk_mib=9333, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep1.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:10:47 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.err deleted file mode 100644 index 3301242..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12216, disk_mib=11651, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:05:42 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=12216, disk_mib=11651, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_Rep2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:14:03 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.err deleted file mode 100644 index bada02c..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6100, disk_mb=6396, disk_mib=6100, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_SPR1.1 - resources: mem_mb=9537, mem_mib=6100, disk_mb=6396, disk_mib=6100, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.1.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:35 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.err deleted file mode 100644 index 9bcf9df..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6101, disk_mb=6397, disk_mib=6101, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_SPR1.2 - resources: mem_mb=9537, mem_mib=6101, disk_mb=6397, disk_mib=6101, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR1.2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:08 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.err deleted file mode 100644 index 293dbd5..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=8022, disk_mib=7651, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:05:42 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.1_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_SPR2.1 - resources: mem_mb=9537, mem_mib=7630, disk_mb=8022, disk_mib=7651, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.1 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.1.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:12:31 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.err deleted file mode 100644 index 3f7903d..0000000 --- a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.err +++ /dev/null @@ -1,49 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=8022, disk_mib=7651, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:05:42 2024] -localrule macs2: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.2_peaks.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_SPR2.2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=8022, disk_mib=7651, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam == "*_spp.out" ]] ; then - if [[ -e /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam ]] ; then - shift=$(awk '{print $3}' /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam | awk -F ',' '{if ($1==146){print $2} else {print $1} }') - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 --extsize ${shift}> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.err - fi - fi - else - if [[ no == "yes" ]] ; then - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.err - else - macs2 callpeak -t /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -c /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -f BAM -g hs -n /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.2 -p 0.1 --keep-dup all --nomodel --extsize=100 > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/logs/Klf4_shUbc9_SPR2.2.err - fi - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:12:30 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.out b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.err deleted file mode 100644 index 429123a..0000000 --- a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.err +++ /dev/null @@ -1,53 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12025, disk_mib=11468, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:27:45 2024] -localrule macs3_CallPeaks: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.out, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/MACS3_ATAC_D0_rep1.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1 - resources: mem_mb=9537, mem_mib=7630, disk_mb=12025, disk_mib=11468, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ yes == "yes" ]]; then - macs3 predictd -f BAMPE -i RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.err | awk '{print$17}') - - if [[ $frag_len -le '0' ]]; then - frag_len=200 - fi - - if [[ yes == "yes" ]]; then - shift_len=$((-1*$frag_len/2)) - else - shift_len='-100' - fi - - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1 -p 0.001 --keep-dup all --nomodel --shift $shift_len --extsize $frag_len >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.err - else - macs3 predictd -f BAM -i RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.err | awk '{print$17}') - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam -f BAM -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1 -p 0.001 --keep-dup all --nomodel >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep1.err - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 11:42:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.out b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.err deleted file mode 100644 index e508280..0000000 --- a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.err +++ /dev/null @@ -1,53 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10754, disk_mib=10256, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:30:45 2024] -localrule macs3_CallPeaks: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.out, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/MACS3_ATAC_D0_rep2.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2 - resources: mem_mb=9537, mem_mib=7630, disk_mb=10754, disk_mib=10256, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ yes == "yes" ]]; then - macs3 predictd -f BAMPE -i RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.err | awk '{print$17}') - - if [[ $frag_len -le '0' ]]; then - frag_len=200 - fi - - if [[ yes == "yes" ]]; then - shift_len=$((-1*$frag_len/2)) - else - shift_len='-100' - fi - - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2 -p 0.001 --keep-dup all --nomodel --shift $shift_len --extsize $frag_len >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.err - else - macs3 predictd -f BAM -i RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.err | awk '{print$17}') - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam -f BAM -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2 -p 0.001 --keep-dup all --nomodel >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep2.err - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 10:42:38 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.out b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.err deleted file mode 100644 index 5729ce9..0000000 --- a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.err +++ /dev/null @@ -1,53 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9524, disk_mib=9083, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 07:47:50 2024] -localrule macs3_CallPeaks: - input: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.out, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/MACS3_ATAC_D0_rep3.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3 - resources: mem_mb=9537, mem_mib=7630, disk_mb=9524, disk_mib=9083, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ yes == "yes" ]]; then - macs3 predictd -f BAMPE -i RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.err | awk '{print$17}') - - if [[ $frag_len -le '0' ]]; then - frag_len=200 - fi - - if [[ yes == "yes" ]]; then - shift_len=$((-1*$frag_len/2)) - else - shift_len='-100' - fi - - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3 -p 0.001 --keep-dup all --nomodel --shift $shift_len --extsize $frag_len >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.err - else - macs3 predictd -f BAM -i RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.err | awk '{print$17}') - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam -f BAM -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3 -p 0.001 --keep-dup all --nomodel >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D0_rep3.err - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 07:58:12 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.out b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.err deleted file mode 100644 index 0e2f100..0000000 --- a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.err +++ /dev/null @@ -1,53 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5065, disk_mb=5310, disk_mib=5065, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:52:51 2024] -localrule macs3_CallPeaks: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.out, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/MACS3_ATAC_D6F_rep1.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1 - resources: mem_mb=9537, mem_mib=5065, disk_mb=5310, disk_mib=5065, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ yes == "yes" ]]; then - macs3 predictd -f BAMPE -i RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.err | awk '{print$17}') - - if [[ $frag_len -le '0' ]]; then - frag_len=200 - fi - - if [[ yes == "yes" ]]; then - shift_len=$((-1*$frag_len/2)) - else - shift_len='-100' - fi - - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1 -p 0.001 --keep-dup all --nomodel --shift $shift_len --extsize $frag_len >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.err - else - macs3 predictd -f BAM -i RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.err | awk '{print$17}') - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam -f BAM -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1 -p 0.001 --keep-dup all --nomodel >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep1.err - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 00:58:24 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.out b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.err deleted file mode 100644 index 64ee511..0000000 --- a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.err +++ /dev/null @@ -1,53 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5250, disk_mb=5504, disk_mib=5250, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:54:49 2024] -localrule macs3_CallPeaks: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.out, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/MACS3_ATAC_D6F_rep2.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2 - resources: mem_mb=9537, mem_mib=5250, disk_mb=5504, disk_mib=5250, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ yes == "yes" ]]; then - macs3 predictd -f BAMPE -i RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.err | awk '{print$17}') - - if [[ $frag_len -le '0' ]]; then - frag_len=200 - fi - - if [[ yes == "yes" ]]; then - shift_len=$((-1*$frag_len/2)) - else - shift_len='-100' - fi - - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2 -p 0.001 --keep-dup all --nomodel --shift $shift_len --extsize $frag_len >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.err - else - macs3 predictd -f BAM -i RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.err | awk '{print$17}') - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam -f BAM -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2 -p 0.001 --keep-dup all --nomodel >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep2.err - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 00:00:37 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.out b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.err deleted file mode 100644 index 1700a92..0000000 --- a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.err +++ /dev/null @@ -1,53 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6182, disk_mb=6482, disk_mib=6182, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 02:11:50 2024] -localrule macs3_CallPeaks: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.out, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/MACS3_ATAC_D6F_rep3.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3 - resources: mem_mb=9537, mem_mib=6182, disk_mb=6482, disk_mib=6182, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ yes == "yes" ]]; then - macs3 predictd -f BAMPE -i RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.err | awk '{print$17}') - - if [[ $frag_len -le '0' ]]; then - frag_len=200 - fi - - if [[ yes == "yes" ]]; then - shift_len=$((-1*$frag_len/2)) - else - shift_len='-100' - fi - - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3 -p 0.001 --keep-dup all --nomodel --shift $shift_len --extsize $frag_len >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.err - else - macs3 predictd -f BAM -i RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.err | awk '{print$17}') - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam -f BAM -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3 -p 0.001 --keep-dup all --nomodel >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6F_rep3.err - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 02:18:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.out b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.err deleted file mode 100644 index 2d03ac7..0000000 --- a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.err +++ /dev/null @@ -1,53 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5709, disk_mb=5986, disk_mib=5709, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:25:43 2024] -localrule macs3_CallPeaks: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.out, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/MACS3_ATAC_D6_rep1.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1 - resources: mem_mb=9537, mem_mib=5709, disk_mb=5986, disk_mib=5709, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ yes == "yes" ]]; then - macs3 predictd -f BAMPE -i RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.err | awk '{print$17}') - - if [[ $frag_len -le '0' ]]; then - frag_len=200 - fi - - if [[ yes == "yes" ]]; then - shift_len=$((-1*$frag_len/2)) - else - shift_len='-100' - fi - - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1 -p 0.001 --keep-dup all --nomodel --shift $shift_len --extsize $frag_len >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.err - else - macs3 predictd -f BAM -i RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.err | awk '{print$17}') - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam -f BAM -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1 -p 0.001 --keep-dup all --nomodel >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep1.err - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 00:32:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.out b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.err deleted file mode 100644 index 4443406..0000000 --- a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.err +++ /dev/null @@ -1,53 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7497, disk_mb=7861, disk_mib=7497, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 05:16:44 2024] -localrule macs3_CallPeaks: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.out, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/MACS3_ATAC_D6_rep2.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2 - resources: mem_mb=9537, mem_mib=7497, disk_mb=7861, disk_mib=7497, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ yes == "yes" ]]; then - macs3 predictd -f BAMPE -i RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.err | awk '{print$17}') - - if [[ $frag_len -le '0' ]]; then - frag_len=200 - fi - - if [[ yes == "yes" ]]; then - shift_len=$((-1*$frag_len/2)) - else - shift_len='-100' - fi - - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2 -p 0.001 --keep-dup all --nomodel --shift $shift_len --extsize $frag_len >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.err - else - macs3 predictd -f BAM -i RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.err | awk '{print$17}') - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam -f BAM -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2 -p 0.001 --keep-dup all --nomodel >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep2.err - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 05:25:08 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.out b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.err deleted file mode 100644 index 08a6251..0000000 --- a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.err +++ /dev/null @@ -1,53 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5850, disk_mb=6134, disk_mib=5850, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:17:48 2024] -localrule macs3_CallPeaks: - input: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam - output: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.out, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.err - jobid: 0 - benchmark: RES_ATAC/06-PeakCalling/Benchmarks/MACS3_ATAC_D6_rep3.bench.txt - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3 - resources: mem_mb=9537, mem_mib=5850, disk_mb=6134, disk_mib=5850, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [[ yes == "yes" ]]; then - macs3 predictd -f BAMPE -i RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.err | awk '{print$17}') - - if [[ $frag_len -le '0' ]]; then - frag_len=200 - fi - - if [[ yes == "yes" ]]; then - shift_len=$((-1*$frag_len/2)) - else - shift_len='-100' - fi - - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam -f BAMPE -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3 -p 0.001 --keep-dup all --nomodel --shift $shift_len --extsize $frag_len >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.err - else - macs3 predictd -f BAM -i RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam -g hs -m 5 50 > RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.out 2> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.err - frag_len=$(grep '# Average insertion length' RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.err | awk '{print$17}') - macs3 callpeak -t RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam -f BAM -g hs -n RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3 -p 0.001 --keep-dup all --nomodel >> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.out 2>> RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/logs/ATAC_D6_rep3.err - fi - - -Activating singularity image epeak.sif -[Thu Sep 12 10:23:48 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.out b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.err deleted file mode 100644 index 17fe601..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=7630, disk_mb=13109, disk_mib=12502, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:33:45 2024] -localrule mark_duplicates: - input: RES_ATAC/02-Mapping/ATAC_D0_rep1_hg38_sort.bam - output: RES_ATAC/03-Deduplication/ATAC_D0_rep1_hg38_sort_dedup.bam, RES_ATAC/03-Deduplication/ATAC_D0_rep1_hg38_sort_dedup.txt - log: RES_ATAC/03-Deduplication/logs/ATAC_D0_rep1_hg38_sort_dedup.out, RES_ATAC/03-Deduplication/logs/ATAC_D0_rep1_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1, REF=hg38 - resources: mem_mb=57220, mem_mib=7630, disk_mb=13109, disk_mib=12502, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (picard MarkDuplicates I=RES_ATAC/02-Mapping/ATAC_D0_rep1_hg38_sort.bam O=RES_ATAC/03-Deduplication/ATAC_D0_rep1_hg38_sort_dedup.bam M=RES_ATAC/03-Deduplication/ATAC_D0_rep1_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index RES_ATAC/03-Deduplication/ATAC_D0_rep1_hg38_sort_dedup.bam) > RES_ATAC/03-Deduplication/logs/ATAC_D0_rep1_hg38_sort_dedup.out 2> RES_ATAC/03-Deduplication/logs/ATAC_D0_rep1_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 11:03:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.err deleted file mode 100644 index bb8561e..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=7630, disk_mb=11660, disk_mib=11120, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 09:42:43 2024] -localrule mark_duplicates: - input: RES_ATAC/02-Mapping/ATAC_D0_rep2_hg38_sort.bam - output: RES_ATAC/03-Deduplication/ATAC_D0_rep2_hg38_sort_dedup.bam, RES_ATAC/03-Deduplication/ATAC_D0_rep2_hg38_sort_dedup.txt - log: RES_ATAC/03-Deduplication/logs/ATAC_D0_rep2_hg38_sort_dedup.out, RES_ATAC/03-Deduplication/logs/ATAC_D0_rep2_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2, REF=hg38 - resources: mem_mb=57220, mem_mib=7630, disk_mb=11660, disk_mib=11120, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (picard MarkDuplicates I=RES_ATAC/02-Mapping/ATAC_D0_rep2_hg38_sort.bam O=RES_ATAC/03-Deduplication/ATAC_D0_rep2_hg38_sort_dedup.bam M=RES_ATAC/03-Deduplication/ATAC_D0_rep2_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index RES_ATAC/03-Deduplication/ATAC_D0_rep2_hg38_sort_dedup.bam) > RES_ATAC/03-Deduplication/logs/ATAC_D0_rep2_hg38_sort_dedup.out 2> RES_ATAC/03-Deduplication/logs/ATAC_D0_rep2_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:09:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.err deleted file mode 100644 index 6010522..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=7630, disk_mb=10361, disk_mib=9882, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 07:05:56 2024] -localrule mark_duplicates: - input: RES_ATAC/02-Mapping/ATAC_D0_rep3_hg38_sort.bam - output: RES_ATAC/03-Deduplication/ATAC_D0_rep3_hg38_sort_dedup.bam, RES_ATAC/03-Deduplication/ATAC_D0_rep3_hg38_sort_dedup.txt - log: RES_ATAC/03-Deduplication/logs/ATAC_D0_rep3_hg38_sort_dedup.out, RES_ATAC/03-Deduplication/logs/ATAC_D0_rep3_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3, REF=hg38 - resources: mem_mb=57220, mem_mib=7630, disk_mb=10361, disk_mib=9882, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (picard MarkDuplicates I=RES_ATAC/02-Mapping/ATAC_D0_rep3_hg38_sort.bam O=RES_ATAC/03-Deduplication/ATAC_D0_rep3_hg38_sort_dedup.bam M=RES_ATAC/03-Deduplication/ATAC_D0_rep3_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index RES_ATAC/03-Deduplication/ATAC_D0_rep3_hg38_sort_dedup.bam) > RES_ATAC/03-Deduplication/logs/ATAC_D0_rep3_hg38_sort_dedup.out 2> RES_ATAC/03-Deduplication/logs/ATAC_D0_rep3_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 07:29:13 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.err deleted file mode 100644 index 26310c4..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=5582, disk_mb=5853, disk_mib=5582, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:29:40 2024] -localrule mark_duplicates: - input: RES_ATAC/02-Mapping/ATAC_D6F_rep1_hg38_sort.bam - output: RES_ATAC/03-Deduplication/ATAC_D6F_rep1_hg38_sort_dedup.bam, RES_ATAC/03-Deduplication/ATAC_D6F_rep1_hg38_sort_dedup.txt - log: RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep1_hg38_sort_dedup.out, RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep1_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1, REF=hg38 - resources: mem_mb=57220, mem_mib=5582, disk_mb=5853, disk_mib=5582, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (picard MarkDuplicates I=RES_ATAC/02-Mapping/ATAC_D6F_rep1_hg38_sort.bam O=RES_ATAC/03-Deduplication/ATAC_D6F_rep1_hg38_sort_dedup.bam M=RES_ATAC/03-Deduplication/ATAC_D6F_rep1_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index RES_ATAC/03-Deduplication/ATAC_D6F_rep1_hg38_sort_dedup.bam) > RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep1_hg38_sort_dedup.out 2> RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep1_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 00:42:15 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.err deleted file mode 100644 index 6ff9ef2..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=5673, disk_mb=5948, disk_mib=5673, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:31:41 2024] -localrule mark_duplicates: - input: RES_ATAC/02-Mapping/ATAC_D6F_rep2_hg38_sort.bam - output: RES_ATAC/03-Deduplication/ATAC_D6F_rep2_hg38_sort_dedup.bam, RES_ATAC/03-Deduplication/ATAC_D6F_rep2_hg38_sort_dedup.txt - log: RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep2_hg38_sort_dedup.out, RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep2_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2, REF=hg38 - resources: mem_mb=57220, mem_mib=5673, disk_mb=5948, disk_mib=5673, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (picard MarkDuplicates I=RES_ATAC/02-Mapping/ATAC_D6F_rep2_hg38_sort.bam O=RES_ATAC/03-Deduplication/ATAC_D6F_rep2_hg38_sort_dedup.bam M=RES_ATAC/03-Deduplication/ATAC_D6F_rep2_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index RES_ATAC/03-Deduplication/ATAC_D6F_rep2_hg38_sort_dedup.bam) > RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep2_hg38_sort_dedup.out 2> RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep2_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 23:44:25 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.err deleted file mode 100644 index 80578a1..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=6721, disk_mb=7047, disk_mib=6721, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 01:43:47 2024] -localrule mark_duplicates: - input: RES_ATAC/02-Mapping/ATAC_D6F_rep3_hg38_sort.bam - output: RES_ATAC/03-Deduplication/ATAC_D6F_rep3_hg38_sort_dedup.bam, RES_ATAC/03-Deduplication/ATAC_D6F_rep3_hg38_sort_dedup.txt - log: RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep3_hg38_sort_dedup.out, RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep3_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3, REF=hg38 - resources: mem_mb=57220, mem_mib=6721, disk_mb=7047, disk_mib=6721, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (picard MarkDuplicates I=RES_ATAC/02-Mapping/ATAC_D6F_rep3_hg38_sort.bam O=RES_ATAC/03-Deduplication/ATAC_D6F_rep3_hg38_sort_dedup.bam M=RES_ATAC/03-Deduplication/ATAC_D6F_rep3_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index RES_ATAC/03-Deduplication/ATAC_D6F_rep3_hg38_sort_dedup.bam) > RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep3_hg38_sort_dedup.out 2> RES_ATAC/03-Deduplication/logs/ATAC_D6F_rep3_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 01:59:03 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.err deleted file mode 100644 index 3facf5e..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=6125, disk_mb=6422, disk_mib=6125, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:59:46 2024] -localrule mark_duplicates: - input: RES_ATAC/02-Mapping/ATAC_D6_rep1_hg38_sort.bam - output: RES_ATAC/03-Deduplication/ATAC_D6_rep1_hg38_sort_dedup.bam, RES_ATAC/03-Deduplication/ATAC_D6_rep1_hg38_sort_dedup.txt - log: RES_ATAC/03-Deduplication/logs/ATAC_D6_rep1_hg38_sort_dedup.out, RES_ATAC/03-Deduplication/logs/ATAC_D6_rep1_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1, REF=hg38 - resources: mem_mb=57220, mem_mib=6125, disk_mb=6422, disk_mib=6125, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (picard MarkDuplicates I=RES_ATAC/02-Mapping/ATAC_D6_rep1_hg38_sort.bam O=RES_ATAC/03-Deduplication/ATAC_D6_rep1_hg38_sort_dedup.bam M=RES_ATAC/03-Deduplication/ATAC_D6_rep1_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index RES_ATAC/03-Deduplication/ATAC_D6_rep1_hg38_sort_dedup.bam) > RES_ATAC/03-Deduplication/logs/ATAC_D6_rep1_hg38_sort_dedup.out 2> RES_ATAC/03-Deduplication/logs/ATAC_D6_rep1_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 00:13:37 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.err deleted file mode 100644 index 2b375e0..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=7630, disk_mb=8547, disk_mib=8152, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 04:43:09 2024] -localrule mark_duplicates: - input: RES_ATAC/02-Mapping/ATAC_D6_rep2_hg38_sort.bam - output: RES_ATAC/03-Deduplication/ATAC_D6_rep2_hg38_sort_dedup.bam, RES_ATAC/03-Deduplication/ATAC_D6_rep2_hg38_sort_dedup.txt - log: RES_ATAC/03-Deduplication/logs/ATAC_D6_rep2_hg38_sort_dedup.out, RES_ATAC/03-Deduplication/logs/ATAC_D6_rep2_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2, REF=hg38 - resources: mem_mb=57220, mem_mib=7630, disk_mb=8547, disk_mib=8152, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (picard MarkDuplicates I=RES_ATAC/02-Mapping/ATAC_D6_rep2_hg38_sort.bam O=RES_ATAC/03-Deduplication/ATAC_D6_rep2_hg38_sort_dedup.bam M=RES_ATAC/03-Deduplication/ATAC_D6_rep2_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index RES_ATAC/03-Deduplication/ATAC_D6_rep2_hg38_sort_dedup.bam) > RES_ATAC/03-Deduplication/logs/ATAC_D6_rep2_hg38_sort_dedup.out 2> RES_ATAC/03-Deduplication/logs/ATAC_D6_rep2_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 05:01:42 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.err deleted file mode 100644 index 0a99a96..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=7630, disk_mb=10009, disk_mib=9546, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 09:46:46 2024] -localrule mark_duplicates: - input: RES_ATAC/02-Mapping/ATAC_D6_rep3_hg38_sort.bam - output: RES_ATAC/03-Deduplication/ATAC_D6_rep3_hg38_sort_dedup.bam, RES_ATAC/03-Deduplication/ATAC_D6_rep3_hg38_sort_dedup.txt - log: RES_ATAC/03-Deduplication/logs/ATAC_D6_rep3_hg38_sort_dedup.out, RES_ATAC/03-Deduplication/logs/ATAC_D6_rep3_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3, REF=hg38 - resources: mem_mb=57220, mem_mib=7630, disk_mb=10009, disk_mib=9546, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (picard MarkDuplicates I=RES_ATAC/02-Mapping/ATAC_D6_rep3_hg38_sort.bam O=RES_ATAC/03-Deduplication/ATAC_D6_rep3_hg38_sort_dedup.bam M=RES_ATAC/03-Deduplication/ATAC_D6_rep3_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index RES_ATAC/03-Deduplication/ATAC_D6_rep3_hg38_sort_dedup.bam) > RES_ATAC/03-Deduplication/logs/ATAC_D6_rep3_hg38_sort_dedup.out 2> RES_ATAC/03-Deduplication/logs/ATAC_D6_rep3_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:05:38 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index cfe5482..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4526, disk_mb=4745, disk_mib=4526, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:31:00 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=hg38 - resources: mem_mb=57220, mem_mib=4526, disk_mb=4745, disk_mib=4526, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:38:54 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index e8811b7..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4571, disk_mb=4793, disk_mib=4571, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:05:10 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=mm10 - resources: mem_mb=57220, mem_mib=4571, disk_mb=4793, disk_mib=4571, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep1_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 21:15:37 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index 6b30bfd..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4770, disk_mb=5001, disk_mib=4770, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:32:02 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=hg38 - resources: mem_mb=57220, mem_mib=4770, disk_mb=5001, disk_mib=4770, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:40:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index 7657e9d..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4734, disk_mb=4963, disk_mib=4734, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:04:11 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=mm10 - resources: mem_mb=57220, mem_mib=4734, disk_mb=4963, disk_mib=4734, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shCtrl_Rep2_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 22:14:56 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index 07cae2e..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=5394, disk_mb=5656, disk_mib=5394, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 15:01:55 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=hg38 - resources: mem_mb=57220, mem_mib=5394, disk_mb=5656, disk_mib=5394, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 15:11:16 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 6b058e3..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=5262, disk_mb=5517, disk_mib=5262, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:31:04 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=mm10 - resources: mem_mb=57220, mem_mib=5262, disk_mb=5517, disk_mib=5262, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep1_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 21:42:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index 358bbbd..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4208, disk_mb=4412, disk_mib=4208, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:38:58 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=hg38 - resources: mem_mb=57220, mem_mib=4208, disk_mb=4412, disk_mib=4208, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:46:30 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index aa0d659..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4278, disk_mb=4485, disk_mib=4278, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 20:41:12 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=mm10 - resources: mem_mb=57220, mem_mib=4278, disk_mb=4485, disk_mib=4278, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/H3K27ac_shUbc9_Rep2_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 20:50:55 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index 6851cc4..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=3909, disk_mb=4098, disk_mib=3909, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:53:01 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep1_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep1_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=hg38 - resources: mem_mb=57220, mem_mib=3909, disk_mb=4098, disk_mib=3909, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep1_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep1_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 15:00:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 538390f..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4289, disk_mb=4497, disk_mib=4289, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:51:05 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep1_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep1_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=mm10 - resources: mem_mb=57220, mem_mib=4289, disk_mb=4497, disk_mib=4289, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep1_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep1_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep1_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 23:00:27 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index fddaf87..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4464, disk_mb=4680, disk_mib=4464, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 15:11:03 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep2_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep2_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=hg38 - resources: mem_mb=57220, mem_mib=4464, disk_mb=4680, disk_mib=4464, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep2_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep2_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 15:19:34 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index b981b98..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=5065, disk_mb=5310, disk_mib=5065, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:41 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep2_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep2_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=mm10 - resources: mem_mb=57220, mem_mib=5065, disk_mb=5310, disk_mib=5065, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shCtrl_Rep2_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep2_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shCtrl_Rep2_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:58:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index bd87e4c..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4465, disk_mb=4681, disk_mib=4465, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Aug 28 14:20:42 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep1_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep1_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=hg38 - resources: mem_mb=57220, mem_mib=4465, disk_mb=4681, disk_mib=4465, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep1_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep1_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Aug 28 14:28:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index c43beb9..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=5014, disk_mb=5257, disk_mib=5014, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:38 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep1_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep1_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=mm10 - resources: mem_mb=57220, mem_mib=5014, disk_mb=5257, disk_mib=5014, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep1_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep1_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep1_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:57:53 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index b887f1b..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4795, disk_mb=5027, disk_mib=4795, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Aug 28 14:20:09 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep2_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep2_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=hg38 - resources: mem_mb=57220, mem_mib=4795, disk_mb=5027, disk_mib=4795, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep2_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep2_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Aug 28 14:29:23 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index eb37e20..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=5460, disk_mb=5725, disk_mib=5460, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:38 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep2_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep2_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=mm10 - resources: mem_mb=57220, mem_mib=5460, disk_mb=5725, disk_mib=5460, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/INPUT_shUbc9_Rep2_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep2_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/INPUT_shUbc9_Rep2_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:59:15 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index 9bc989b..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=3768, disk_mb=3950, disk_mib=3768, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:25:58 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep1_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep1_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=hg38 - resources: mem_mb=57220, mem_mib=3768, disk_mb=3950, disk_mib=3768, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep1_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep1_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:32:59 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index d8a380e..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4241, disk_mb=4447, disk_mib=4241, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:11:07 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep1_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep1_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=mm10 - resources: mem_mb=57220, mem_mib=4241, disk_mb=4447, disk_mib=4241, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep1_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep1_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep1_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 21:22:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index e59e46f..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=3447, disk_mb=3614, disk_mib=3447, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:32:03 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep2_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep2_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=hg38 - resources: mem_mb=57220, mem_mib=3447, disk_mb=3614, disk_mib=3447, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep2_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep2_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:38:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index 7879798..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=3818, disk_mb=4003, disk_mib=3818, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 20:37:27 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep2_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep2_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=mm10 - resources: mem_mb=57220, mem_mib=3818, disk_mb=4003, disk_mib=3818, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shCtrl_Rep2_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep2_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shCtrl_Rep2_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 20:48:02 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index 74ac7b2..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=3895, disk_mb=4084, disk_mib=3895, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:48:55 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep1_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep1_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=hg38 - resources: mem_mb=57220, mem_mib=3895, disk_mb=4084, disk_mib=3895, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep1_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep1_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:56:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 12ce8aa..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4316, disk_mb=4525, disk_mib=4316, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:27:05 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep1_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep1_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=mm10 - resources: mem_mb=57220, mem_mib=4316, disk_mb=4525, disk_mib=4316, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep1_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep1_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep1_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 22:39:27 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index 6d61465..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=4735, disk_mb=4965, disk_mib=4735, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 15:11:52 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_hg38_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_hg38_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_hg38_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep2_hg38_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep2_hg38_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=hg38 - resources: mem_mb=57220, mem_mib=4735, disk_mb=4965, disk_mib=4735, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_hg38_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_hg38_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_hg38_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_hg38_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep2_hg38_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep2_hg38_sort_dedup.err - -Activating singularity image epeak.sif -[Tue Aug 27 15:20:27 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 3b2315e..0000000 --- a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=57220, mem_mib=5289, disk_mb=5545, disk_mib=5289, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:21:04 2024] -localrule mark_duplicates: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_mm10_sort.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_mm10_sort_dedup.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_mm10_sort_dedup.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep2_mm10_sort_dedup.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep2_mm10_sort_dedup.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=mm10 - resources: mem_mb=57220, mem_mib=5289, disk_mb=5545, disk_mib=5289, tmpdir=/pasteur/appa/scratch/rlegendr, mem=60G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (PicardCommandLine MarkDuplicates I=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/02-Mapping/Klf4_shUbc9_Rep2_mm10_sort.bam O=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_mm10_sort_dedup.bam M=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_mm10_sort_dedup.txt REMOVE_DUPLICATES=true TMP_DIR=$TMPDIR && samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_mm10_sort_dedup.bam) > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep2_mm10_sort_dedup.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/logs/Klf4_shUbc9_Rep2_mm10_sort_dedup.err - -Activating singularity image epeak.sif -[Wed Sep 11 22:35:29 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep1.FORM=narrow.err b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep1.FORM=narrow.err deleted file mode 100644 index 82d227f..0000000 --- a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep1.FORM=narrow.err +++ /dev/null @@ -1,40 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:16:02 2024] -localrule merge_peakcaller: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak - output: RES_ATAC/13-MergePeaks/ATAC_D0_rep1_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep1_all_narrow.bed - log: RES_ATAC/13-MergePeaks/logs/ATAC_D0_rep1_mergePeaks_narrow.out, RES_ATAC/13-MergePeaks/logs/ATAC_D0_rep1_mergePeaks_narrow.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - for file in RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak; do - cat "$file" >> RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep1_all_narrow.bed_tmp - done - - bedtools sort -i RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep1_all_narrow.bed_tmp > RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep1_all_narrow.bed - - bedtools merge -c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max -i RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep1_all_narrow.bed > RES_ATAC/13-MergePeaks/ATAC_D0_rep1_mergePeaks.narrowPeak 2> RES_ATAC/13-MergePeaks/logs/ATAC_D0_rep1_mergePeaks_narrow.err - - rm RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep1_all_narrow.bed_tmp - - -Activating singularity image epeak.sif -[Thu Sep 12 12:16:05 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep1.FORM=narrow.out b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep1.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep2.FORM=narrow.err b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep2.FORM=narrow.err deleted file mode 100644 index 709fd4b..0000000 --- a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep2.FORM=narrow.err +++ /dev/null @@ -1,40 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:11:42 2024] -localrule merge_peakcaller: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak - output: RES_ATAC/13-MergePeaks/ATAC_D0_rep2_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep2_all_narrow.bed - log: RES_ATAC/13-MergePeaks/logs/ATAC_D0_rep2_mergePeaks_narrow.out, RES_ATAC/13-MergePeaks/logs/ATAC_D0_rep2_mergePeaks_narrow.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - for file in RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak; do - cat "$file" >> RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep2_all_narrow.bed_tmp - done - - bedtools sort -i RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep2_all_narrow.bed_tmp > RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep2_all_narrow.bed - - bedtools merge -c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max -i RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep2_all_narrow.bed > RES_ATAC/13-MergePeaks/ATAC_D0_rep2_mergePeaks.narrowPeak 2> RES_ATAC/13-MergePeaks/logs/ATAC_D0_rep2_mergePeaks_narrow.err - - rm RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep2_all_narrow.bed_tmp - - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:44 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep2.FORM=narrow.out b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep2.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep3.FORM=narrow.err b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep3.FORM=narrow.err deleted file mode 100644 index 4d7a078..0000000 --- a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep3.FORM=narrow.err +++ /dev/null @@ -1,40 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 08:25:51 2024] -localrule merge_peakcaller: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak - output: RES_ATAC/13-MergePeaks/ATAC_D0_rep3_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep3_all_narrow.bed - log: RES_ATAC/13-MergePeaks/logs/ATAC_D0_rep3_mergePeaks_narrow.out, RES_ATAC/13-MergePeaks/logs/ATAC_D0_rep3_mergePeaks_narrow.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - for file in RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak; do - cat "$file" >> RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep3_all_narrow.bed_tmp - done - - bedtools sort -i RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep3_all_narrow.bed_tmp > RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep3_all_narrow.bed - - bedtools merge -c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max -i RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep3_all_narrow.bed > RES_ATAC/13-MergePeaks/ATAC_D0_rep3_mergePeaks.narrowPeak 2> RES_ATAC/13-MergePeaks/logs/ATAC_D0_rep3_mergePeaks_narrow.err - - rm RES_ATAC/13-MergePeaks/concat/ATAC_D0_rep3_all_narrow.bed_tmp - - -Activating singularity image epeak.sif -[Thu Sep 12 08:25:53 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep3.FORM=narrow.out b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep3.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.err b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.err deleted file mode 100644 index 6fafbfe..0000000 --- a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.err +++ /dev/null @@ -1,40 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 01:24:42 2024] -localrule merge_peakcaller: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak - output: RES_ATAC/13-MergePeaks/ATAC_D6F_rep1_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep1_all_narrow.bed - log: RES_ATAC/13-MergePeaks/logs/ATAC_D6F_rep1_mergePeaks_narrow.out, RES_ATAC/13-MergePeaks/logs/ATAC_D6F_rep1_mergePeaks_narrow.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - for file in RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak; do - cat "$file" >> RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep1_all_narrow.bed_tmp - done - - bedtools sort -i RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep1_all_narrow.bed_tmp > RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep1_all_narrow.bed - - bedtools merge -c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max -i RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep1_all_narrow.bed > RES_ATAC/13-MergePeaks/ATAC_D6F_rep1_mergePeaks.narrowPeak 2> RES_ATAC/13-MergePeaks/logs/ATAC_D6F_rep1_mergePeaks_narrow.err - - rm RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep1_all_narrow.bed_tmp - - -Activating singularity image epeak.sif -[Thu Sep 12 01:24:45 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.out b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.err b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.err deleted file mode 100644 index 33021fc..0000000 --- a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.err +++ /dev/null @@ -1,40 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:28:49 2024] -localrule merge_peakcaller: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak - output: RES_ATAC/13-MergePeaks/ATAC_D6F_rep2_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep2_all_narrow.bed - log: RES_ATAC/13-MergePeaks/logs/ATAC_D6F_rep2_mergePeaks_narrow.out, RES_ATAC/13-MergePeaks/logs/ATAC_D6F_rep2_mergePeaks_narrow.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - for file in RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak; do - cat "$file" >> RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep2_all_narrow.bed_tmp - done - - bedtools sort -i RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep2_all_narrow.bed_tmp > RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep2_all_narrow.bed - - bedtools merge -c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max -i RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep2_all_narrow.bed > RES_ATAC/13-MergePeaks/ATAC_D6F_rep2_mergePeaks.narrowPeak 2> RES_ATAC/13-MergePeaks/logs/ATAC_D6F_rep2_mergePeaks_narrow.err - - rm RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep2_all_narrow.bed_tmp - - -Activating singularity image epeak.sif -[Thu Sep 12 00:28:51 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.out b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.err b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.err deleted file mode 100644 index b851bee..0000000 --- a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.err +++ /dev/null @@ -1,40 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 02:47:56 2024] -localrule merge_peakcaller: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak - output: RES_ATAC/13-MergePeaks/ATAC_D6F_rep3_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep3_all_narrow.bed - log: RES_ATAC/13-MergePeaks/logs/ATAC_D6F_rep3_mergePeaks_narrow.out, RES_ATAC/13-MergePeaks/logs/ATAC_D6F_rep3_mergePeaks_narrow.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - for file in RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak; do - cat "$file" >> RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep3_all_narrow.bed_tmp - done - - bedtools sort -i RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep3_all_narrow.bed_tmp > RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep3_all_narrow.bed - - bedtools merge -c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max -i RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep3_all_narrow.bed > RES_ATAC/13-MergePeaks/ATAC_D6F_rep3_mergePeaks.narrowPeak 2> RES_ATAC/13-MergePeaks/logs/ATAC_D6F_rep3_mergePeaks_narrow.err - - rm RES_ATAC/13-MergePeaks/concat/ATAC_D6F_rep3_all_narrow.bed_tmp - - -Activating singularity image epeak.sif -[Thu Sep 12 02:47:59 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.out b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep1.FORM=narrow.err b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep1.FORM=narrow.err deleted file mode 100644 index 17805f1..0000000 --- a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep1.FORM=narrow.err +++ /dev/null @@ -1,40 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 01:00:41 2024] -localrule merge_peakcaller: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak - output: RES_ATAC/13-MergePeaks/ATAC_D6_rep1_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep1_all_narrow.bed - log: RES_ATAC/13-MergePeaks/logs/ATAC_D6_rep1_mergePeaks_narrow.out, RES_ATAC/13-MergePeaks/logs/ATAC_D6_rep1_mergePeaks_narrow.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - for file in RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak; do - cat "$file" >> RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep1_all_narrow.bed_tmp - done - - bedtools sort -i RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep1_all_narrow.bed_tmp > RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep1_all_narrow.bed - - bedtools merge -c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max -i RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep1_all_narrow.bed > RES_ATAC/13-MergePeaks/ATAC_D6_rep1_mergePeaks.narrowPeak 2> RES_ATAC/13-MergePeaks/logs/ATAC_D6_rep1_mergePeaks_narrow.err - - rm RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep1_all_narrow.bed_tmp - - -Activating singularity image epeak.sif -[Thu Sep 12 01:00:43 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep1.FORM=narrow.out b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep1.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep2.FORM=narrow.err b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep2.FORM=narrow.err deleted file mode 100644 index 19bb7b2..0000000 --- a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep2.FORM=narrow.err +++ /dev/null @@ -1,40 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 05:52:44 2024] -localrule merge_peakcaller: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/13-MergePeaks/ATAC_D6_rep2_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep2_all_narrow.bed - log: RES_ATAC/13-MergePeaks/logs/ATAC_D6_rep2_mergePeaks_narrow.out, RES_ATAC/13-MergePeaks/logs/ATAC_D6_rep2_mergePeaks_narrow.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - for file in RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak; do - cat "$file" >> RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep2_all_narrow.bed_tmp - done - - bedtools sort -i RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep2_all_narrow.bed_tmp > RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep2_all_narrow.bed - - bedtools merge -c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max -i RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep2_all_narrow.bed > RES_ATAC/13-MergePeaks/ATAC_D6_rep2_mergePeaks.narrowPeak 2> RES_ATAC/13-MergePeaks/logs/ATAC_D6_rep2_mergePeaks_narrow.err - - rm RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep2_all_narrow.bed_tmp - - -Activating singularity image epeak.sif -[Thu Sep 12 05:52:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep2.FORM=narrow.out b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep2.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep3.FORM=narrow.err b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep3.FORM=narrow.err deleted file mode 100644 index a8ad5e9..0000000 --- a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep3.FORM=narrow.err +++ /dev/null @@ -1,40 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:44:43 2024] -localrule merge_peakcaller: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak - output: RES_ATAC/13-MergePeaks/ATAC_D6_rep3_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep3_all_narrow.bed - log: RES_ATAC/13-MergePeaks/logs/ATAC_D6_rep3_mergePeaks_narrow.out, RES_ATAC/13-MergePeaks/logs/ATAC_D6_rep3_mergePeaks_narrow.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - for file in RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak; do - cat "$file" >> RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep3_all_narrow.bed_tmp - done - - bedtools sort -i RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep3_all_narrow.bed_tmp > RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep3_all_narrow.bed - - bedtools merge -c 4,5,6,7,8,9,10 -o collapse,max,collapse,mean,mean,mean,max -i RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep3_all_narrow.bed > RES_ATAC/13-MergePeaks/ATAC_D6_rep3_mergePeaks.narrowPeak 2> RES_ATAC/13-MergePeaks/logs/ATAC_D6_rep3_mergePeaks_narrow.err - - rm RES_ATAC/13-MergePeaks/concat/ATAC_D6_rep3_all_narrow.bed_tmp - - -Activating singularity image epeak.sif -[Thu Sep 12 10:44:45 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep3.FORM=narrow.out b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep3.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/metrics_chipr/metrics_chipr_CALLER=genrich.MOD=narrow.FORM=narrow.err b/logs/slurm/metrics_chipr/metrics_chipr_CALLER=genrich.MOD=narrow.FORM=narrow.err deleted file mode 100644 index 672745f..0000000 --- a/logs/slurm/metrics_chipr/metrics_chipr_CALLER=genrich.MOD=narrow.FORM=narrow.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:17:01 2024] -localrule metrics_chipr: - input: RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_log.txt - output: RES_ATAC2/CHIPR_genrich_narrow_narrow_metrics.out - log: RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/log_Chipr_metrics.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -RuleException: -ValueError in file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/metrics_chipr.rules, line 83: -All arrays must be of the same length - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/metrics_chipr.rules", line 83, in __rule_metrics_chipr - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/miniconda3/envs/s8/lib/python3.12/site-packages/pandas/core/frame.py", line 778, in __init__ - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/miniconda3/envs/s8/lib/python3.12/site-packages/pandas/core/internals/construction.py", line 448, in dict_to_mgr - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/miniconda3/envs/s8/lib/python3.12/site-packages/pandas/core/internals/construction.py", line 677, in _extract_index -[Wed Sep 11 15:17:01 2024] -Error in rule metrics_chipr: - jobid: 0 - input: RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_log.txt - output: RES_ATAC2/CHIPR_genrich_narrow_narrow_metrics.out - log: RES_ATAC2/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/log_Chipr_metrics.out (check log file(s) for error details) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/metrics_chipr/metrics_chipr_CALLER=genrich.MOD=narrow.FORM=narrow.out b/logs/slurm/metrics_chipr/metrics_chipr_CALLER=genrich.MOD=narrow.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/metrics_chipr/metrics_chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err b/logs/slurm/metrics_chipr/metrics_chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err deleted file mode 100644 index 7815878..0000000 --- a/logs/slurm/metrics_chipr/metrics_chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:17:00 2024] -localrule metrics_chipr: - input: RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_log.txt - output: RES_ATAC2/CHIPR_lanceOtron_narrow_narrow_metrics.out - log: RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/log_Chipr_metrics.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -RuleException: -ValueError in file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/metrics_chipr.rules, line 83: -All arrays must be of the same length - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/metrics_chipr.rules", line 83, in __rule_metrics_chipr - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/miniconda3/envs/s8/lib/python3.12/site-packages/pandas/core/frame.py", line 778, in __init__ - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/miniconda3/envs/s8/lib/python3.12/site-packages/pandas/core/internals/construction.py", line 448, in dict_to_mgr - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/miniconda3/envs/s8/lib/python3.12/site-packages/pandas/core/internals/construction.py", line 677, in _extract_index -[Wed Sep 11 15:17:00 2024] -Error in rule metrics_chipr: - jobid: 0 - input: RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_log.txt - output: RES_ATAC2/CHIPR_lanceOtron_narrow_narrow_metrics.out - log: RES_ATAC2/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/log_Chipr_metrics.out (check log file(s) for error details) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/metrics_chipr/metrics_chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.out b/logs/slurm/metrics_chipr/metrics_chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/metrics_chipr/metrics_chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err b/logs/slurm/metrics_chipr/metrics_chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err deleted file mode 100644 index 2dc1e97..0000000 --- a/logs/slurm/metrics_chipr/metrics_chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 15:17:00 2024] -localrule metrics_chipr: - input: RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_log.txt - output: RES_ATAC2/CHIPR_macs3_CallPeak_noModel_narrow_metrics.out - log: RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/log_Chipr_metrics.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -RuleException: -ValueError in file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/metrics_chipr.rules, line 83: -All arrays must be of the same length - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/metrics_chipr.rules", line 83, in __rule_metrics_chipr - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/miniconda3/envs/s8/lib/python3.12/site-packages/pandas/core/frame.py", line 778, in __init__ - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/miniconda3/envs/s8/lib/python3.12/site-packages/pandas/core/internals/construction.py", line 448, in dict_to_mgr - File "/pasteur/zeus/projets/p01/BioIT/Rachelbis/miniconda3/envs/s8/lib/python3.12/site-packages/pandas/core/internals/construction.py", line 677, in _extract_index -[Wed Sep 11 15:17:00 2024] -Error in rule metrics_chipr: - jobid: 0 - input: RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_log.txt, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_log.txt - output: RES_ATAC2/CHIPR_macs3_CallPeak_noModel_narrow_metrics.out - log: RES_ATAC2/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/log_Chipr_metrics.out (check log file(s) for error details) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/metrics_chipr/metrics_chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.out b/logs/slurm/metrics_chipr/metrics_chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/metrics_chipr/metrics_chipr_unique.err b/logs/slurm/metrics_chipr/metrics_chipr_unique.err deleted file mode 100644 index f583d61..0000000 --- a/logs/slurm/metrics_chipr/metrics_chipr_unique.err +++ /dev/null @@ -1,26 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 09:57:26 2024] -localrule metrics_chipr: - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/CHIPR_metrics.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/08-ReproduciblePeaks/macs2_narrow/Chipr/CHIPR_metrics.out - jobid: 0 - reason: Forced execution - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -[Thu Sep 5 09:57:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/metrics_chipr/metrics_chipr_unique.out b/logs/slurm/metrics_chipr/metrics_chipr_unique.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/metrics_peaks/metrics_peaks_unique.err b/logs/slurm/metrics_peaks/metrics_peaks_unique.err deleted file mode 100644 index dda107f..0000000 --- a/logs/slurm/metrics_peaks/metrics_peaks_unique.err +++ /dev/null @@ -1,27 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:16:51 2024] -localrule metrics_peaks: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR1.1vsSPR1.2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_SPR2.1vsSPR2.2_mm10_narrow_idr0.05.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/IDR_metrics.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/logs/IDR_metrics.out - jobid: 0 - reason: Forced execution - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -[Thu Sep 12 11:16:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/metrics_peaks/metrics_peaks_unique.out b/logs/slurm/metrics_peaks/metrics_peaks_unique.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/multiqc/multiqc_unique.err b/logs/slurm/multiqc/multiqc_unique.err deleted file mode 100644 index bcd14d1..0000000 --- a/logs/slurm/multiqc/multiqc_unique.err +++ /dev/null @@ -1,29 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10555, disk_mib=10067, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 13:15:51 2024] -localrule multiqc: - input: RES_ATAC/00-Fastqc/ATAC_D6_rep1_R1_001_fastqc.done, RES_ATAC/00-Fastqc/ATAC_D6F_rep1_R1_001_fastqc.done, RES_ATAC/00-Fastqc/ATAC_D6F_rep3_R1_001_fastqc.done, RES_ATAC/00-Fastqc/ATAC_D6F_rep2_R1_001_fastqc.done, RES_ATAC/00-Fastqc/ATAC_D6_rep3_R1_001_fastqc.done, RES_ATAC/00-Fastqc/ATAC_D0_rep2_R1_001_fastqc.done, RES_ATAC/00-Fastqc/ATAC_D0_rep1_R1_001_fastqc.done, RES_ATAC/00-Fastqc/ATAC_D6_rep2_R1_001_fastqc.done, RES_ATAC/00-Fastqc/ATAC_D0_rep3_R1_001_fastqc.done, RES_ATAC/12-IGV/ATAC_D6_rep1_hg38_coverage.bw, RES_ATAC/12-IGV/ATAC_D6F_rep1_hg38_coverage.bw, RES_ATAC/12-IGV/ATAC_D6F_rep3_hg38_coverage.bw, RES_ATAC/12-IGV/ATAC_D6F_rep2_hg38_coverage.bw, RES_ATAC/12-IGV/ATAC_D6_rep3_hg38_coverage.bw, RES_ATAC/12-IGV/ATAC_D0_rep2_hg38_coverage.bw, RES_ATAC/12-IGV/ATAC_D0_rep1_hg38_coverage.bw, RES_ATAC/12-IGV/ATAC_D6_rep2_hg38_coverage.bw, RES_ATAC/12-IGV/ATAC_D0_rep3_hg38_coverage.bw, RES_ATAC/05-QC/Complexity/ATAC_D6_rep1_hg38_metrics.txt, RES_ATAC/05-QC/Complexity/ATAC_D6F_rep1_hg38_metrics.txt, RES_ATAC/05-QC/Complexity/ATAC_D6F_rep3_hg38_metrics.txt, RES_ATAC/05-QC/Complexity/ATAC_D6F_rep2_hg38_metrics.txt, RES_ATAC/05-QC/Complexity/ATAC_D6_rep3_hg38_metrics.txt, RES_ATAC/05-QC/Complexity/ATAC_D0_rep2_hg38_metrics.txt, RES_ATAC/05-QC/Complexity/ATAC_D0_rep1_hg38_metrics.txt, RES_ATAC/05-QC/Complexity/ATAC_D6_rep2_hg38_metrics.txt, RES_ATAC/05-QC/Complexity/ATAC_D0_rep3_hg38_metrics.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep1_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep1_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep3_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6F_rep2_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep3_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep2_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep1_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D6_rep2_hg38_fragmentSizeDistribution.txt, RES_ATAC/05-QC/FragmentSizeDistribution/ATAC_D0_rep3_hg38_fragmentSizeDistribution.txt, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep2_dedup_sort.bw, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep1_dedup_sort.bw, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D0_rep3_dedup_sort.bw, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep1_dedup_sort.bw, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep1_dedup_sort.bw, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep3_dedup_sort.bw, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6F_rep2_dedup_sort.bw, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep3_dedup_sort.bw, RES_ATAC/06-PeakCalling/lanceOtron_narrow/inputs/ATAC_D6_rep2_dedup_sort.bw, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak, RES_ATAC/macs3_CallPeak_noModel_narrow_Peaks_metrics_mqc.out, RES_ATAC/genrich_narrow_narrow_Peaks_metrics_mqc.out, RES_ATAC/lanceOtron_narrow_narrow_Peaks_metrics_mqc.out, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_log.txt, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_log.txt, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_log.txt, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_log.txt, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_log.txt, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_log.txt, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_log.txt, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_log.txt, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_log.txt, RES_ATAC/13-MergePeaks/ATAC_D0_rep2_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/ATAC_D0_rep1_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/ATAC_D0_rep3_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/ATAC_D6_rep1_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/ATAC_D6F_rep1_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/ATAC_D6F_rep3_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/ATAC_D6F_rep2_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/ATAC_D6_rep3_mergePeaks.narrowPeak, RES_ATAC/13-MergePeaks/ATAC_D6_rep2_mergePeaks.narrowPeak, RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed, RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed, RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed, RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff, RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff, RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.gff, RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_Matrix_Optimal_Peak.mtx, RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_Matrix_Optimal_Peak.mtx, RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_Matrix_Optimal_Peak.mtx, RES_ATAC/10-DifferentialAnalysis/macs3_CallPeak_noModel/ATAC_Limma_scale/ATAC_Stat_report_Limma_scale.html, RES_ATAC/10-DifferentialAnalysis/genrich_narrow/ATAC_Limma_scale/ATAC_Stat_report_Limma_scale.html, RES_ATAC/10-DifferentialAnalysis/lanceOtron_narrow/ATAC_Limma_scale/ATAC_Stat_report_Limma_scale.html - output: RES_ATAC/11-Multiqc/multiqc/multiqc_report.html - log: RES_ATAC/11-Multiqc/multiqc.log - jobid: 0 - reason: Forced execution - resources: mem_mb=9537, mem_mib=7630, disk_mb=10555, disk_mib=10067, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - multiqc RES_ATAC/ -o RES_ATAC/11-Multiqc/multiqc -f -e macs2 -x 03-Deduplication/*spikes* -x 02-Mapping/*_spike* -c config/multiqc_atac_config.yaml 2> RES_ATAC/11-Multiqc/multiqc.log - -Activating singularity image epeak.sif -[Thu Sep 12 13:16:13 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/multiqc/multiqc_unique.out b/logs/slurm/multiqc/multiqc_unique.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.err deleted file mode 100644 index 864f314..0000000 --- a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4439, disk_mb=4654, disk_mib=4439, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule plotFingerprint: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep1_mm10_fingerprint.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep1_mm10_fingerprint_rawcounts.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shCtrl_Rep1_mm10_Fingerprint.out - jobid: 0 - reason: Forced execution - wildcards: IP=H3K27ac_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=4439, disk_mb=4654, disk_mib=4439, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - if [[ ${#infiles[@]} > 1 ]] ; then - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - INPUT=${infiles[1]} ; INPUT=$(basename ${INPUT%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep1_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep1_mm10_fingerprint_rawcounts.txt --labels ${IP} ${INPUT} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shCtrl_Rep1_mm10_Fingerprint.out - else - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep1_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep1_mm10_fingerprint_rawcounts.txt --labels ${IP} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shCtrl_Rep1_mm10_Fingerprint.out - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:08:01 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.out b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.err deleted file mode 100644 index 2af1f1a..0000000 --- a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4285, disk_mb=4493, disk_mib=4285, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:09 2024] -localrule plotFingerprint: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep2_mm10_fingerprint.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep2_mm10_fingerprint_rawcounts.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shCtrl_Rep2_mm10_Fingerprint.out - jobid: 0 - reason: Forced execution - wildcards: IP=H3K27ac_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=4285, disk_mb=4493, disk_mib=4285, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - if [[ ${#infiles[@]} > 1 ]] ; then - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - INPUT=${infiles[1]} ; INPUT=$(basename ${INPUT%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep2_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep2_mm10_fingerprint_rawcounts.txt --labels ${IP} ${INPUT} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shCtrl_Rep2_mm10_Fingerprint.out - else - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep2_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shCtrl_Rep2_mm10_fingerprint_rawcounts.txt --labels ${IP} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shCtrl_Rep2_mm10_Fingerprint.out - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:08:01 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.out b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.err deleted file mode 100644 index 0cca8d6..0000000 --- a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5001, disk_mb=5243, disk_mib=5001, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule plotFingerprint: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep1_mm10_fingerprint.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep1_mm10_fingerprint_rawcounts.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shUbc9_Rep1_mm10_Fingerprint.out - jobid: 0 - reason: Forced execution - wildcards: IP=H3K27ac_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=5001, disk_mb=5243, disk_mib=5001, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - if [[ ${#infiles[@]} > 1 ]] ; then - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - INPUT=${infiles[1]} ; INPUT=$(basename ${INPUT%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep1_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep1_mm10_fingerprint_rawcounts.txt --labels ${IP} ${INPUT} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shUbc9_Rep1_mm10_Fingerprint.out - else - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep1_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep1_mm10_fingerprint_rawcounts.txt --labels ${IP} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shUbc9_Rep1_mm10_Fingerprint.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:07:13 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.out b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.err deleted file mode 100644 index 5bd0703..0000000 --- a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4768, disk_mb=4999, disk_mib=4768, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule plotFingerprint: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep2_mm10_fingerprint.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep2_mm10_fingerprint_rawcounts.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shUbc9_Rep2_mm10_Fingerprint.out - jobid: 0 - reason: Forced execution - wildcards: IP=H3K27ac_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=4768, disk_mb=4999, disk_mib=4768, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - if [[ ${#infiles[@]} > 1 ]] ; then - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - INPUT=${infiles[1]} ; INPUT=$(basename ${INPUT%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep2_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep2_mm10_fingerprint_rawcounts.txt --labels ${IP} ${INPUT} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shUbc9_Rep2_mm10_Fingerprint.out - else - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep2_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/H3K27ac_shUbc9_Rep2_mm10_fingerprint_rawcounts.txt --labels ${IP} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/H3K27ac_shUbc9_Rep2_mm10_Fingerprint.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:06:56 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.out b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.err deleted file mode 100644 index 128af95..0000000 --- a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5292, disk_mb=5549, disk_mib=5292, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:05:06 2024] -localrule plotFingerprint: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep1_mm10_fingerprint.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep1_mm10_fingerprint_rawcounts.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shCtrl_Rep1_mm10_Fingerprint.out - jobid: 0 - reason: Forced execution - wildcards: IP=Klf4_shCtrl_Rep1 - resources: mem_mb=9537, mem_mib=5292, disk_mb=5549, disk_mib=5292, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - if [[ ${#infiles[@]} > 1 ]] ; then - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - INPUT=${infiles[1]} ; INPUT=$(basename ${INPUT%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep1_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep1_mm10_fingerprint_rawcounts.txt --labels ${IP} ${INPUT} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shCtrl_Rep1_mm10_Fingerprint.out - else - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep1_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep1_mm10_fingerprint_rawcounts.txt --labels ${IP} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shCtrl_Rep1_mm10_Fingerprint.out - fi - -Activating singularity image epeak.sif -[Wed Sep 11 23:08:15 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.out b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.err deleted file mode 100644 index bf0171c..0000000 --- a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5708, disk_mb=5985, disk_mib=5708, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:04 2024] -localrule plotFingerprint: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep2_mm10_fingerprint.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep2_mm10_fingerprint_rawcounts.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shCtrl_Rep2_mm10_Fingerprint.out - jobid: 0 - reason: Forced execution - wildcards: IP=Klf4_shCtrl_Rep2 - resources: mem_mb=9537, mem_mib=5708, disk_mb=5985, disk_mib=5708, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - if [[ ${#infiles[@]} > 1 ]] ; then - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - INPUT=${infiles[1]} ; INPUT=$(basename ${INPUT%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep2_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep2_mm10_fingerprint_rawcounts.txt --labels ${IP} ${INPUT} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shCtrl_Rep2_mm10_Fingerprint.out - else - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep2_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shCtrl_Rep2_mm10_fingerprint_rawcounts.txt --labels ${IP} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shCtrl_Rep2_mm10_Fingerprint.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:07:18 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.out b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.err deleted file mode 100644 index 49b8842..0000000 --- a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5873, disk_mb=6158, disk_mib=5873, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:01 2024] -localrule plotFingerprint: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep1_mm10_fingerprint.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep1_mm10_fingerprint_rawcounts.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shUbc9_Rep1_mm10_Fingerprint.out - jobid: 0 - reason: Forced execution - wildcards: IP=Klf4_shUbc9_Rep1 - resources: mem_mb=9537, mem_mib=5873, disk_mb=6158, disk_mib=5873, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - if [[ ${#infiles[@]} > 1 ]] ; then - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - INPUT=${infiles[1]} ; INPUT=$(basename ${INPUT%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep1_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep1_mm10_fingerprint_rawcounts.txt --labels ${IP} ${INPUT} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shUbc9_Rep1_mm10_Fingerprint.out - else - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep1_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep1_mm10_fingerprint_rawcounts.txt --labels ${IP} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shUbc9_Rep1_mm10_Fingerprint.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:07:16 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.out b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.err deleted file mode 100644 index 9702dee..0000000 --- a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7364, disk_mb=7721, disk_mib=7364, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:05:39 2024] -localrule plotFingerprint: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep2_mm10_fingerprint.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep2_mm10_fingerprint_rawcounts.txt - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shUbc9_Rep2_mm10_Fingerprint.out - jobid: 0 - reason: Forced execution - wildcards: IP=Klf4_shUbc9_Rep2 - resources: mem_mb=9537, mem_mib=7364, disk_mb=7721, disk_mib=7364, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - if [[ ${#infiles[@]} > 1 ]] ; then - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - INPUT=${infiles[1]} ; INPUT=$(basename ${INPUT%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep2_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep2_mm10_fingerprint_rawcounts.txt --labels ${IP} ${INPUT} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shUbc9_Rep2_mm10_Fingerprint.out - else - IP=${infiles[0]} ; IP=$(basename ${IP%_sort*}) - plotFingerprint --bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam --plotFile /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep2_mm10_fingerprint.pdf --outRawCounts /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/Klf4_shUbc9_Rep2_mm10_fingerprint_rawcounts.txt --labels ${IP} --numberOfProcessors 1 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/Fingerprint/logs/Klf4_shUbc9_Rep2_mm10_Fingerprint.out - fi - -Activating singularity image epeak.sif -[Thu Sep 12 11:09:35 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.out b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 789a104..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:38 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep1_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep1_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shCtrl_Rep1_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep1_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep1_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shCtrl_Rep1_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 12 10:48:13 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index 2ed008e..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:37 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep2_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep2_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shCtrl_Rep2_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep2_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shCtrl_Rep2_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shCtrl_Rep2_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 12 10:48:12 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 386e48b..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:41 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep1_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep1_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shUbc9_Rep1_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep1_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep1_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shUbc9_Rep1_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 12 10:48:13 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index b8a3651..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:55:11 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep2_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep2_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shUbc9_Rep2_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep2_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/H3K27ac_shUbc9_Rep2_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/H3K27ac_shUbc9_Rep2_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Wed Sep 11 22:56:37 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 8f4caca..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 19:05:32 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep1_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep1_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shCtrl_Rep1_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep1_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep1_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shCtrl_Rep1_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 5 19:06:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index e7890e7..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 18:55:32 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep2_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep2_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shCtrl_Rep2_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep2_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shCtrl_Rep2_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shCtrl_Rep2_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 5 18:56:48 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 48c2ba3..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 19:22:36 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep1_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep1_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shUbc9_Rep1_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep1_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep1_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shUbc9_Rep1_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 5 19:23:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 583902a..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 5 21:21:41 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep2_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep2_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shUbc9_Rep2_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep2_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/INPUT_shUbc9_Rep2_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP2/05-QC/GeneBody/logs/INPUT_shUbc9_Rep2_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 5 21:22:50 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index e3cfb09..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:41 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep1_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep1_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shCtrl_Rep1_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep1_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep1_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shCtrl_Rep1_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 12 10:48:10 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index be03f8b..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:56:02 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep2_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep2_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shCtrl_Rep2_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep2_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shCtrl_Rep2_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shCtrl_Rep2_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Wed Sep 11 22:56:59 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 8698ff1..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:38 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep1_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep1_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shUbc9_Rep1_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep1_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep1_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shUbc9_Rep1_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 12 10:48:12 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index b438c61..0000000 --- a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:46:41 2024] -localrule plotHeatmap: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep2_mm10.mat.gz - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep2_mm10_GeneBody.pdf - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shUbc9_Rep2_mm10_GeneBody.out - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - plotHeatmap -m /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep2_mm10.mat.gz -out /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/Klf4_shUbc9_Rep2_mm10_GeneBody.pdf 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/GeneBody/logs/Klf4_shUbc9_Rep2_mm10_GeneBody.out - -Activating singularity image epeak.sif -[Thu Sep 12 10:48:14 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.err b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.err deleted file mode 100644 index 7f2b5f9..0000000 --- a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.err +++ /dev/null @@ -1,152 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=95367, mem_mib=4941, disk_mb=5180, disk_mib=4941, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:20:11 2024] -localrule preIDR_PPR: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - jobid: 0 - reason: Forced execution - wildcards: IP=H3K27ac_shCtrl - resources: mem_mb=95367, mem_mib=4941, disk_mb=5180, disk_mib=4941, tmpdir=/pasteur/appa/scratch/rlegendr, mem=100G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set -euxo pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam" - outfiles=($tmp) - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - - FILE1=${outfiles[0]} - FILE2=${outfiles[1]} - FILE_Pool=${outfiles[2]} - echo "Delete old files in case of rerun..." > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - rm ${FILE_Pool%%.*}_header.sam 2> /dev/null || true - rm ${FILE_Pool%%.*}00 2> /dev/null || true - rm ${FILE_Pool%%.*}01 2> /dev/null || true - - - echo "Merging BAM files for pseudoreplicates..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - samtools merge $FILE_Pool ${infiles[0]} ${infiles[1]} - - echo "Spliting bam file $FILE_Pool ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - samtools view -H $FILE_Pool >> ${FILE_Pool%%.*}_header.sam - nlinesPPR=$(samtools view ${FILE_Pool} | wc -l ) # Number of reads in the BAM file - nlinesPPR=$(( ($nlinesPPR+1)/2 )) # half that number - - # This will shuffle the lines in the file and split it into two SAM files - samtools view ${FILE_Pool} | shuf | split -d -l ${nlinesPPR} - ${FILE_Pool%%.*} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}00 | samtools view -bS | samtools sort -o ${FILE1} - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}01 | samtools view -bS | samtools sort -o ${FILE2} - - echo "Indexing self pseudos-replicates Bamfiles ${FILE1} ${FILE2}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - samtools index ${FILE1} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - samtools index ${FILE2} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - - # Cleaning of useless files - rm ${FILE_Pool%%.*}_header.sam - rm ${FILE_Pool%%.*}00 - rm ${FILE_Pool%%.*}01 - - - if [[ ${#infiles[@]} > 3 ]] ; then - FILE3=${infiles[2]} - n=1 - for $FILEN in ${infiles[0]} ${infiles[1]} ; do - FILE_Pool=${FILE1/Rep1/Rep${n}3-Pool} - samtools merge $FILE_Pool $FILEN $FILE2 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - - echo "Spliting bam file $FILE_Pool ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - nlinesPPR=$(samtools view $FILE_Pool | wc -l ) # Number of reads in the BAM file - nlinesPPR=$(( ($nlinesPPR+1)/2 )) # half that number - - # This will shuffle the lines in the file and split it into two SAM files - samtools view $FILE_Pool | shuf | split -d -l ${nlinesPPR} - ${FILE_Pool%%.*} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - - - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}00 | samtools view -bS - | samtools sort -o ${FILE_Pool/Pool/PPR1} - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}01 | samtools view -bS - | samtools sort -o ${FILE_Pool/Pool/PPR2} - - echo "Indexing self pseudos-replicates Bamfiles ${file}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - samtools index ${FILE_Pool/Pool/PPR1} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - samtools index ${FILE_Pool/Pool/PPR2} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - - # Cleaning of useless files - rm ${FILE_Pool%%.*}_header.sam - rm ${FILE_Pool%%.*}00 - rm ${FILE_Pool%%.*}01 - - n++ - done - - echo "Merging BAM files on maxi pool for pseudoreplicates..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - FILE_MaxPool=${outfiles[4]} - samtools merge ${FILE_MaxPool}_tmp ${infiles[0]} ${infiles[1]} ${infiles[2]} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - samtools sort -o ${FILE_MaxPool} ${FILE_MaxPool}_tmp 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - samtools index ${FILE_MaxPool} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_PPR.o - - - # Cleaning of useless files - rm ${FILE_MaxPool}_tmp - - fi - - -Activating singularity image epeak.sif -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam' -+ outfiles=($tmp) -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam' -+ infiles=($tmp) -+ FILE1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -+ FILE2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -+ FILE_Pool=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'Merging BAM files for pseudoreplicates...' -+ samtools merge /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ nlinesPPR=75959747 -+ nlinesPPR=37979874 -+ split -d -l 37979874 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 11 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 11 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions01 -+ [[ 2 > 3 ]] -[Wed Sep 11 22:52:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.out b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.err b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.err deleted file mode 100644 index 5bd8bb6..0000000 --- a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.err +++ /dev/null @@ -1,152 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=95367, mem_mib=4944, disk_mb=5184, disk_mib=4944, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:48:25 2024] -localrule preIDR_PPR: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - jobid: 0 - reason: Forced execution - wildcards: IP=H3K27ac_shUbc9 - resources: mem_mb=95367, mem_mib=4944, disk_mb=5184, disk_mib=4944, tmpdir=/pasteur/appa/scratch/rlegendr, mem=100G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set -euxo pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam" - outfiles=($tmp) - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - - FILE1=${outfiles[0]} - FILE2=${outfiles[1]} - FILE_Pool=${outfiles[2]} - echo "Delete old files in case of rerun..." > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - rm ${FILE_Pool%%.*}_header.sam 2> /dev/null || true - rm ${FILE_Pool%%.*}00 2> /dev/null || true - rm ${FILE_Pool%%.*}01 2> /dev/null || true - - - echo "Merging BAM files for pseudoreplicates..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - samtools merge $FILE_Pool ${infiles[0]} ${infiles[1]} - - echo "Spliting bam file $FILE_Pool ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - samtools view -H $FILE_Pool >> ${FILE_Pool%%.*}_header.sam - nlinesPPR=$(samtools view ${FILE_Pool} | wc -l ) # Number of reads in the BAM file - nlinesPPR=$(( ($nlinesPPR+1)/2 )) # half that number - - # This will shuffle the lines in the file and split it into two SAM files - samtools view ${FILE_Pool} | shuf | split -d -l ${nlinesPPR} - ${FILE_Pool%%.*} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}00 | samtools view -bS | samtools sort -o ${FILE1} - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}01 | samtools view -bS | samtools sort -o ${FILE2} - - echo "Indexing self pseudos-replicates Bamfiles ${FILE1} ${FILE2}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - samtools index ${FILE1} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - samtools index ${FILE2} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - - # Cleaning of useless files - rm ${FILE_Pool%%.*}_header.sam - rm ${FILE_Pool%%.*}00 - rm ${FILE_Pool%%.*}01 - - - if [[ ${#infiles[@]} > 3 ]] ; then - FILE3=${infiles[2]} - n=1 - for $FILEN in ${infiles[0]} ${infiles[1]} ; do - FILE_Pool=${FILE1/Rep1/Rep${n}3-Pool} - samtools merge $FILE_Pool $FILEN $FILE2 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - - echo "Spliting bam file $FILE_Pool ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - nlinesPPR=$(samtools view $FILE_Pool | wc -l ) # Number of reads in the BAM file - nlinesPPR=$(( ($nlinesPPR+1)/2 )) # half that number - - # This will shuffle the lines in the file and split it into two SAM files - samtools view $FILE_Pool | shuf | split -d -l ${nlinesPPR} - ${FILE_Pool%%.*} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - - - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}00 | samtools view -bS - | samtools sort -o ${FILE_Pool/Pool/PPR1} - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}01 | samtools view -bS - | samtools sort -o ${FILE_Pool/Pool/PPR2} - - echo "Indexing self pseudos-replicates Bamfiles ${file}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - samtools index ${FILE_Pool/Pool/PPR1} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - samtools index ${FILE_Pool/Pool/PPR2} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - - # Cleaning of useless files - rm ${FILE_Pool%%.*}_header.sam - rm ${FILE_Pool%%.*}00 - rm ${FILE_Pool%%.*}01 - - n++ - done - - echo "Merging BAM files on maxi pool for pseudoreplicates..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - FILE_MaxPool=${outfiles[4]} - samtools merge ${FILE_MaxPool}_tmp ${infiles[0]} ${infiles[1]} ${infiles[2]} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - samtools sort -o ${FILE_MaxPool} ${FILE_MaxPool}_tmp 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - samtools index ${FILE_MaxPool} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_PPR.o - - - # Cleaning of useless files - rm ${FILE_MaxPool}_tmp - - fi - - -Activating singularity image epeak.sif -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam' -+ outfiles=($tmp) -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam' -+ infiles=($tmp) -+ FILE1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -+ FILE2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -+ FILE_Pool=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'Merging BAM files for pseudoreplicates...' -+ samtools merge /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ nlinesPPR=76433857 -+ nlinesPPR=38216929 -+ split -d -l 38216929 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 11 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 11 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions01 -+ [[ 2 > 3 ]] -[Wed Sep 11 22:20:11 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.out b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.err b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.err deleted file mode 100644 index b47651a..0000000 --- a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.err +++ /dev/null @@ -1,152 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=95367, mem_mib=6418, disk_mb=6729, disk_mib=6418, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:30:11 2024] -localrule preIDR_PPR: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - jobid: 0 - reason: Forced execution - wildcards: IP=Klf4_shCtrl - resources: mem_mb=95367, mem_mib=6418, disk_mb=6729, disk_mib=6418, tmpdir=/pasteur/appa/scratch/rlegendr, mem=100G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set -euxo pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam" - outfiles=($tmp) - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - - FILE1=${outfiles[0]} - FILE2=${outfiles[1]} - FILE_Pool=${outfiles[2]} - echo "Delete old files in case of rerun..." > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - rm ${FILE_Pool%%.*}_header.sam 2> /dev/null || true - rm ${FILE_Pool%%.*}00 2> /dev/null || true - rm ${FILE_Pool%%.*}01 2> /dev/null || true - - - echo "Merging BAM files for pseudoreplicates..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - samtools merge $FILE_Pool ${infiles[0]} ${infiles[1]} - - echo "Spliting bam file $FILE_Pool ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - samtools view -H $FILE_Pool >> ${FILE_Pool%%.*}_header.sam - nlinesPPR=$(samtools view ${FILE_Pool} | wc -l ) # Number of reads in the BAM file - nlinesPPR=$(( ($nlinesPPR+1)/2 )) # half that number - - # This will shuffle the lines in the file and split it into two SAM files - samtools view ${FILE_Pool} | shuf | split -d -l ${nlinesPPR} - ${FILE_Pool%%.*} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}00 | samtools view -bS | samtools sort -o ${FILE1} - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}01 | samtools view -bS | samtools sort -o ${FILE2} - - echo "Indexing self pseudos-replicates Bamfiles ${FILE1} ${FILE2}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - samtools index ${FILE1} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - samtools index ${FILE2} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - - # Cleaning of useless files - rm ${FILE_Pool%%.*}_header.sam - rm ${FILE_Pool%%.*}00 - rm ${FILE_Pool%%.*}01 - - - if [[ ${#infiles[@]} > 3 ]] ; then - FILE3=${infiles[2]} - n=1 - for $FILEN in ${infiles[0]} ${infiles[1]} ; do - FILE_Pool=${FILE1/Rep1/Rep${n}3-Pool} - samtools merge $FILE_Pool $FILEN $FILE2 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - - echo "Spliting bam file $FILE_Pool ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - nlinesPPR=$(samtools view $FILE_Pool | wc -l ) # Number of reads in the BAM file - nlinesPPR=$(( ($nlinesPPR+1)/2 )) # half that number - - # This will shuffle the lines in the file and split it into two SAM files - samtools view $FILE_Pool | shuf | split -d -l ${nlinesPPR} - ${FILE_Pool%%.*} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - - - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}00 | samtools view -bS - | samtools sort -o ${FILE_Pool/Pool/PPR1} - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}01 | samtools view -bS - | samtools sort -o ${FILE_Pool/Pool/PPR2} - - echo "Indexing self pseudos-replicates Bamfiles ${file}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - samtools index ${FILE_Pool/Pool/PPR1} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - samtools index ${FILE_Pool/Pool/PPR2} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - - # Cleaning of useless files - rm ${FILE_Pool%%.*}_header.sam - rm ${FILE_Pool%%.*}00 - rm ${FILE_Pool%%.*}01 - - n++ - done - - echo "Merging BAM files on maxi pool for pseudoreplicates..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - FILE_MaxPool=${outfiles[4]} - samtools merge ${FILE_MaxPool}_tmp ${infiles[0]} ${infiles[1]} ${infiles[2]} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - samtools sort -o ${FILE_MaxPool} ${FILE_MaxPool}_tmp 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - samtools index ${FILE_MaxPool} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_PPR.o - - - # Cleaning of useless files - rm ${FILE_MaxPool}_tmp - - fi - - -Activating singularity image epeak.sif -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam' -+ outfiles=($tmp) -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam' -+ infiles=($tmp) -+ FILE1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -+ FILE2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -+ FILE_Pool=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'Merging BAM files for pseudoreplicates...' -+ samtools merge /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ nlinesPPR=107917984 -+ nlinesPPR=53958992 -+ split -d -l 53958992 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 16 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 16 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPR2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_PPRPool_mm10_sort_dedup_biasedRegions01 -+ [[ 2 > 3 ]] -[Wed Sep 11 22:10:32 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.out b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.err b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.err deleted file mode 100644 index b761fee..0000000 --- a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.err +++ /dev/null @@ -1,152 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=95367, mem_mib=7630, disk_mb=8124, disk_mib=7748, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:47:25 2024] -localrule preIDR_PPR: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - jobid: 0 - reason: Forced execution - wildcards: IP=Klf4_shUbc9 - resources: mem_mb=95367, mem_mib=7630, disk_mb=8124, disk_mib=7748, tmpdir=/pasteur/appa/scratch/rlegendr, mem=100G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set -euxo pipefail - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam" - outfiles=($tmp) - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam" - infiles=($tmp) - - FILE1=${outfiles[0]} - FILE2=${outfiles[1]} - FILE_Pool=${outfiles[2]} - echo "Delete old files in case of rerun..." > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - rm ${FILE_Pool%%.*}_header.sam 2> /dev/null || true - rm ${FILE_Pool%%.*}00 2> /dev/null || true - rm ${FILE_Pool%%.*}01 2> /dev/null || true - - - echo "Merging BAM files for pseudoreplicates..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - samtools merge $FILE_Pool ${infiles[0]} ${infiles[1]} - - echo "Spliting bam file $FILE_Pool ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - samtools view -H $FILE_Pool >> ${FILE_Pool%%.*}_header.sam - nlinesPPR=$(samtools view ${FILE_Pool} | wc -l ) # Number of reads in the BAM file - nlinesPPR=$(( ($nlinesPPR+1)/2 )) # half that number - - # This will shuffle the lines in the file and split it into two SAM files - samtools view ${FILE_Pool} | shuf | split -d -l ${nlinesPPR} - ${FILE_Pool%%.*} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}00 | samtools view -bS | samtools sort -o ${FILE1} - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}01 | samtools view -bS | samtools sort -o ${FILE2} - - echo "Indexing self pseudos-replicates Bamfiles ${FILE1} ${FILE2}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - samtools index ${FILE1} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - samtools index ${FILE2} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - - # Cleaning of useless files - rm ${FILE_Pool%%.*}_header.sam - rm ${FILE_Pool%%.*}00 - rm ${FILE_Pool%%.*}01 - - - if [[ ${#infiles[@]} > 3 ]] ; then - FILE3=${infiles[2]} - n=1 - for $FILEN in ${infiles[0]} ${infiles[1]} ; do - FILE_Pool=${FILE1/Rep1/Rep${n}3-Pool} - samtools merge $FILE_Pool $FILEN $FILE2 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - - echo "Spliting bam file $FILE_Pool ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - nlinesPPR=$(samtools view $FILE_Pool | wc -l ) # Number of reads in the BAM file - nlinesPPR=$(( ($nlinesPPR+1)/2 )) # half that number - - # This will shuffle the lines in the file and split it into two SAM files - samtools view $FILE_Pool | shuf | split -d -l ${nlinesPPR} - ${FILE_Pool%%.*} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - - - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}00 | samtools view -bS - | samtools sort -o ${FILE_Pool/Pool/PPR1} - cat ${FILE_Pool%%.*}_header.sam ${FILE_Pool%%.*}01 | samtools view -bS - | samtools sort -o ${FILE_Pool/Pool/PPR2} - - echo "Indexing self pseudos-replicates Bamfiles ${file}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - samtools index ${FILE_Pool/Pool/PPR1} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - samtools index ${FILE_Pool/Pool/PPR2} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - - # Cleaning of useless files - rm ${FILE_Pool%%.*}_header.sam - rm ${FILE_Pool%%.*}00 - rm ${FILE_Pool%%.*}01 - - n++ - done - - echo "Merging BAM files on maxi pool for pseudoreplicates..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - FILE_MaxPool=${outfiles[4]} - samtools merge ${FILE_MaxPool}_tmp ${infiles[0]} ${infiles[1]} ${infiles[2]} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - samtools sort -o ${FILE_MaxPool} ${FILE_MaxPool}_tmp 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - samtools index ${FILE_MaxPool} 2>> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_PPR.o - - - # Cleaning of useless files - rm ${FILE_MaxPool}_tmp - - fi - - -Activating singularity image epeak.sif -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam' -+ outfiles=($tmp) -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam' -+ infiles=($tmp) -+ FILE1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -+ FILE2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -+ FILE_Pool=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'Merging BAM files for pseudoreplicates...' -+ samtools merge /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ nlinesPPR=132164940 -+ nlinesPPR=66082470 -+ split -d -l 66082470 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 19 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 19 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPR2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_PPRPool_mm10_sort_dedup_biasedRegions01 -+ [[ 2 > 3 ]] -[Wed Sep 11 23:37:11 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.out b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.err b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.err deleted file mode 100644 index 4d65f70..0000000 --- a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.err +++ /dev/null @@ -1,161 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=4941, disk_mb=5180, disk_mib=4941, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:20:11 2024] -localrule preIDR_SPR: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_SPR.o - jobid: 0 - reason: Forced execution - wildcards: IP=H3K27ac_shCtrl - resources: mem_mb=47684, mem_mib=4941, disk_mb=5180, disk_mib=4941, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set -euxo pipefail - i=1 - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam" - outfiles=($tmp) - - for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam ; do - - if [ $i -eq 1 ] - then - SPR="SPR1" ; SPR1=${outfiles[0]} ; SPR2=${outfiles[1]} - - elif [ $i -eq 2 ] - then - SPR="SPR2" ; SPR1=${outfiles[2]} ; SPR2=${outfiles[3]} - else - SPR="SPR3"; SPR1=${outfiles[3]} ; SPR2=${outfiles[4]} - fi - - echo "Delete old files in case of rerun..." > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_SPR.o - rm ${file%.*}_header.sam 2> /dev/null || true - rm ${file%.*}00 2> /dev/null || true - rm ${file%.*}01 2> /dev/null || true - - echo "starting $SPR ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_SPR.o - - samtools view -H ${file} > ${file%.*}_header.sam - - echo "Spliting bam file ${file} ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_SPR.o - - nlinesSPR=$(samtools view ${file} | wc -l ) # Number of reads in the BAM file - - nlinesSPR=$(( (${nlinesSPR}+1)/2 )) # half that number - - samtools view ${file} | shuf | split -d -l ${nlinesSPR} - ${file%.*} # This will shuffle the lines in the file and split it into two SAM files - - cat ${file%.*}_header.sam ${file%.*}00 | samtools view -bS | samtools sort -o ${SPR1} - cat ${file%.*}_header.sam ${file%.*}01 | samtools view -bS | samtools sort -o ${SPR2} - - - echo "Indexing self pseudos-replicates Bamfiles ${file}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_preIDR_SPR.o - samtools index ${SPR1} - samtools index ${SPR2} - - # Cleaning of useless files - rm ${file%.*}_header.sam - rm ${file%.*}00 - rm ${file%.*}01 - i=$((i + 1)) - - done - - - -Activating singularity image epeak.sif -+ i=1 -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam' -+ outfiles=($tmp) -+ for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ '[' 1 -eq 1 ']' -+ SPR=SPR1 -+ SPR1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ SPR2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'starting SPR1 ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam ...' -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -+ nlinesSPR=39085913 -+ nlinesSPR=19542957 -+ split -d -l 19542957 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 5 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 5 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions01 -+ i=2 -+ for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ '[' 2 -eq 1 ']' -+ '[' 2 -eq 2 ']' -+ SPR=SPR2 -+ SPR1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ SPR2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'starting SPR2 ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam ...' -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ nlinesSPR=36873834 -+ nlinesSPR=18436917 -+ split -d -l 18436917 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 5 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 5 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions01 -+ i=3 -[Wed Sep 11 22:44:03 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.out b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.err b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.err deleted file mode 100644 index 264b02e..0000000 --- a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.err +++ /dev/null @@ -1,161 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=4944, disk_mb=5184, disk_mib=4944, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:48:13 2024] -localrule preIDR_SPR: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_SPR.o - jobid: 0 - reason: Forced execution - wildcards: IP=H3K27ac_shUbc9 - resources: mem_mb=47684, mem_mib=4944, disk_mb=5184, disk_mib=4944, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set -euxo pipefail - i=1 - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam" - outfiles=($tmp) - - for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam ; do - - if [ $i -eq 1 ] - then - SPR="SPR1" ; SPR1=${outfiles[0]} ; SPR2=${outfiles[1]} - - elif [ $i -eq 2 ] - then - SPR="SPR2" ; SPR1=${outfiles[2]} ; SPR2=${outfiles[3]} - else - SPR="SPR3"; SPR1=${outfiles[3]} ; SPR2=${outfiles[4]} - fi - - echo "Delete old files in case of rerun..." > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_SPR.o - rm ${file%.*}_header.sam 2> /dev/null || true - rm ${file%.*}00 2> /dev/null || true - rm ${file%.*}01 2> /dev/null || true - - echo "starting $SPR ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_SPR.o - - samtools view -H ${file} > ${file%.*}_header.sam - - echo "Spliting bam file ${file} ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_SPR.o - - nlinesSPR=$(samtools view ${file} | wc -l ) # Number of reads in the BAM file - - nlinesSPR=$(( (${nlinesSPR}+1)/2 )) # half that number - - samtools view ${file} | shuf | split -d -l ${nlinesSPR} - ${file%.*} # This will shuffle the lines in the file and split it into two SAM files - - cat ${file%.*}_header.sam ${file%.*}00 | samtools view -bS | samtools sort -o ${SPR1} - cat ${file%.*}_header.sam ${file%.*}01 | samtools view -bS | samtools sort -o ${SPR2} - - - echo "Indexing self pseudos-replicates Bamfiles ${file}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_preIDR_SPR.o - samtools index ${SPR1} - samtools index ${SPR2} - - # Cleaning of useless files - rm ${file%.*}_header.sam - rm ${file%.*}00 - rm ${file%.*}01 - i=$((i + 1)) - - done - - - -Activating singularity image epeak.sif -+ i=1 -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam' -+ outfiles=($tmp) -+ for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ '[' 1 -eq 1 ']' -+ SPR=SPR1 -+ SPR1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ SPR2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'starting SPR1 ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam ...' -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -+ nlinesSPR=40637398 -+ nlinesSPR=20318699 -+ split -d -l 20318699 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 6 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 6 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions01 -+ i=2 -+ for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ '[' 2 -eq 1 ']' -+ '[' 2 -eq 2 ']' -+ SPR=SPR2 -+ SPR1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ SPR2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'starting SPR2 ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam ...' -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ nlinesSPR=35796459 -+ nlinesSPR=17898230 -+ split -d -l 17898230 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 5 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 5 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions01 -+ i=3 -[Wed Sep 11 22:12:24 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.out b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.err b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.err deleted file mode 100644 index 228b446..0000000 --- a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.err +++ /dev/null @@ -1,161 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=6418, disk_mb=6729, disk_mib=6418, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:30:11 2024] -localrule preIDR_SPR: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_SPR.o - jobid: 0 - reason: Forced execution - wildcards: IP=Klf4_shCtrl - resources: mem_mb=47684, mem_mib=6418, disk_mb=6729, disk_mib=6418, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set -euxo pipefail - i=1 - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam" - outfiles=($tmp) - - for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam ; do - - if [ $i -eq 1 ] - then - SPR="SPR1" ; SPR1=${outfiles[0]} ; SPR2=${outfiles[1]} - - elif [ $i -eq 2 ] - then - SPR="SPR2" ; SPR1=${outfiles[2]} ; SPR2=${outfiles[3]} - else - SPR="SPR3"; SPR1=${outfiles[3]} ; SPR2=${outfiles[4]} - fi - - echo "Delete old files in case of rerun..." > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_SPR.o - rm ${file%.*}_header.sam 2> /dev/null || true - rm ${file%.*}00 2> /dev/null || true - rm ${file%.*}01 2> /dev/null || true - - echo "starting $SPR ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_SPR.o - - samtools view -H ${file} > ${file%.*}_header.sam - - echo "Spliting bam file ${file} ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_SPR.o - - nlinesSPR=$(samtools view ${file} | wc -l ) # Number of reads in the BAM file - - nlinesSPR=$(( (${nlinesSPR}+1)/2 )) # half that number - - samtools view ${file} | shuf | split -d -l ${nlinesSPR} - ${file%.*} # This will shuffle the lines in the file and split it into two SAM files - - cat ${file%.*}_header.sam ${file%.*}00 | samtools view -bS | samtools sort -o ${SPR1} - cat ${file%.*}_header.sam ${file%.*}01 | samtools view -bS | samtools sort -o ${SPR2} - - - echo "Indexing self pseudos-replicates Bamfiles ${file}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_preIDR_SPR.o - samtools index ${SPR1} - samtools index ${SPR2} - - # Cleaning of useless files - rm ${file%.*}_header.sam - rm ${file%.*}00 - rm ${file%.*}01 - i=$((i + 1)) - - done - - - -Activating singularity image epeak.sif -+ i=1 -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam' -+ outfiles=($tmp) -+ for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ '[' 1 -eq 1 ']' -+ SPR=SPR1 -+ SPR1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ SPR2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'starting SPR1 ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam ...' -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -+ nlinesSPR=57028974 -+ nlinesSPR=28514487 -+ split -d -l 28514487 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 8 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 8 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions01 -+ i=2 -+ for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ '[' 2 -eq 1 ']' -+ '[' 2 -eq 2 ']' -+ SPR=SPR2 -+ SPR1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ SPR2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'starting SPR2 ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam ...' -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ nlinesSPR=50889010 -+ nlinesSPR=25444505 -+ split -d -l 25444505 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 7 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 7 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions01 -+ i=3 -[Wed Sep 11 22:01:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.out b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.err b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.err deleted file mode 100644 index 13ba740..0000000 --- a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.err +++ /dev/null @@ -1,161 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=47684, mem_mib=7630, disk_mb=8124, disk_mib=7748, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:47:10 2024] -localrule preIDR_SPR: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_SPR.o - jobid: 0 - reason: Forced execution - wildcards: IP=Klf4_shUbc9 - resources: mem_mb=47684, mem_mib=7630, disk_mb=8124, disk_mib=7748, tmpdir=/pasteur/appa/scratch/rlegendr, mem=50G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set -euxo pipefail - i=1 - tmp="/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam" - outfiles=($tmp) - - for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam ; do - - if [ $i -eq 1 ] - then - SPR="SPR1" ; SPR1=${outfiles[0]} ; SPR2=${outfiles[1]} - - elif [ $i -eq 2 ] - then - SPR="SPR2" ; SPR1=${outfiles[2]} ; SPR2=${outfiles[3]} - else - SPR="SPR3"; SPR1=${outfiles[3]} ; SPR2=${outfiles[4]} - fi - - echo "Delete old files in case of rerun..." > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_SPR.o - rm ${file%.*}_header.sam 2> /dev/null || true - rm ${file%.*}00 2> /dev/null || true - rm ${file%.*}01 2> /dev/null || true - - echo "starting $SPR ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_SPR.o - - samtools view -H ${file} > ${file%.*}_header.sam - - echo "Spliting bam file ${file} ..." >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_SPR.o - - nlinesSPR=$(samtools view ${file} | wc -l ) # Number of reads in the BAM file - - nlinesSPR=$(( (${nlinesSPR}+1)/2 )) # half that number - - samtools view ${file} | shuf | split -d -l ${nlinesSPR} - ${file%.*} # This will shuffle the lines in the file and split it into two SAM files - - cat ${file%.*}_header.sam ${file%.*}00 | samtools view -bS | samtools sort -o ${SPR1} - cat ${file%.*}_header.sam ${file%.*}01 | samtools view -bS | samtools sort -o ${SPR2} - - - echo "Indexing self pseudos-replicates Bamfiles ${file}" >> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_preIDR_SPR.o - samtools index ${SPR1} - samtools index ${SPR2} - - # Cleaning of useless files - rm ${file%.*}_header.sam - rm ${file%.*}00 - rm ${file%.*}01 - i=$((i + 1)) - - done - - - -Activating singularity image epeak.sif -+ i=1 -+ tmp='/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam' -+ outfiles=($tmp) -+ for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ '[' 1 -eq 1 ']' -+ SPR=SPR1 -+ SPR1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ SPR2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'starting SPR1 ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam ...' -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -+ nlinesSPR=59189549 -+ nlinesSPR=29594775 -+ split -d -l 29594775 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 8 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 8 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR1.2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions01 -+ i=2 -+ for file in /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ '[' 2 -eq 1 ']' -+ '[' 2 -eq 2 ']' -+ SPR=SPR2 -+ SPR1=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ SPR2=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Delete old files in case of rerun...' -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_header.sam -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions00 -+ true -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions01 -+ true -+ echo 'starting SPR2 ...' -+ samtools view -H /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ echo 'Spliting bam file /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam ...' -++ wc -l -++ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ nlinesSPR=72975391 -+ nlinesSPR=36487696 -+ split -d -l 36487696 - /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions -+ shuf -+ samtools view /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions00 -[bam_sort_core] merging from 10 files and 1 in-memory blocks... -+ samtools sort -o /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ samtools view -bS -+ cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_header.sam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions01 -[bam_sort_core] merging from 10 files and 1 in-memory blocks... -+ echo 'Indexing self pseudos-replicates Bamfiles /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam' -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.1_mm10_sort_dedup_biasedRegions.bam -+ samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_SPR2.2_mm10_sort_dedup_biasedRegions.bam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_header.sam -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions00 -+ rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions01 -+ i=3 -[Wed Sep 11 23:25:34 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.out b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.err deleted file mode 100644 index 0b1b7e1..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=12926, disk_mib=12328, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:04:16 2024] -localrule remove_biasedRegions: - input: RES_ATAC/03-Deduplication/ATAC_D0_rep1_hg38_sort_dedup.bam - output: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam - log: RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.out, RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=12926, disk_mib=12328, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam RES_ATAC/03-Deduplication/ATAC_D0_rep1_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam) && (samtools index RES_ATAC/04-NobiasedRegions/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.bam > RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.out) 2> RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep1_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 11:26:44 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.err deleted file mode 100644 index a773013..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=11536, disk_mib=11002, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:09:51 2024] -localrule remove_biasedRegions: - input: RES_ATAC/03-Deduplication/ATAC_D0_rep2_hg38_sort_dedup.bam - output: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam - log: RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.out, RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=11536, disk_mib=11002, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam RES_ATAC/03-Deduplication/ATAC_D0_rep2_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam) && (samtools index RES_ATAC/04-NobiasedRegions/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.bam > RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.out) 2> RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep2_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:29:36 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.err deleted file mode 100644 index 2a8c852..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10212, disk_mib=9739, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 07:29:45 2024] -localrule remove_biasedRegions: - input: RES_ATAC/03-Deduplication/ATAC_D0_rep3_hg38_sort_dedup.bam - output: RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam - log: RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.out, RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D0_rep3, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=10212, disk_mib=9739, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam RES_ATAC/03-Deduplication/ATAC_D0_rep3_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam) && (samtools index RES_ATAC/04-NobiasedRegions/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.bam > RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.out) 2> RES_ATAC/04-NobiasedRegions/logs/ATAC_D0_rep3_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 07:46:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.err deleted file mode 100644 index 3928254..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5397, disk_mb=5659, disk_mib=5397, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:42:47 2024] -localrule remove_biasedRegions: - input: RES_ATAC/03-Deduplication/ATAC_D6F_rep1_hg38_sort_dedup.bam - output: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam - log: RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.out, RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=5397, disk_mb=5659, disk_mib=5397, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam RES_ATAC/03-Deduplication/ATAC_D6F_rep1_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam) && (samtools index RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.bam > RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.out) 2> RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep1_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 00:52:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.err deleted file mode 100644 index 8f1959b..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5600, disk_mb=5871, disk_mib=5600, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:44:48 2024] -localrule remove_biasedRegions: - input: RES_ATAC/03-Deduplication/ATAC_D6F_rep2_hg38_sort_dedup.bam - output: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam - log: RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.out, RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=5600, disk_mb=5871, disk_mib=5600, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam RES_ATAC/03-Deduplication/ATAC_D6F_rep2_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam) && (samtools index RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.bam > RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.out) 2> RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep2_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 23:54:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.err deleted file mode 100644 index 359eaba..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6590, disk_mb=6910, disk_mib=6590, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 01:59:50 2024] -localrule remove_biasedRegions: - input: RES_ATAC/03-Deduplication/ATAC_D6F_rep3_hg38_sort_dedup.bam - output: RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam - log: RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.out, RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6F_rep3, REF=hg38 - resources: mem_mb=9537, mem_mib=6590, disk_mb=6910, disk_mib=6590, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam RES_ATAC/03-Deduplication/ATAC_D6F_rep3_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam) && (samtools index RES_ATAC/04-NobiasedRegions/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.bam > RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.out) 2> RES_ATAC/04-NobiasedRegions/logs/ATAC_D6F_rep3_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 02:11:16 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.err deleted file mode 100644 index a445d77..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6096, disk_mb=6392, disk_mib=6096, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 00:14:48 2024] -localrule remove_biasedRegions: - input: RES_ATAC/03-Deduplication/ATAC_D6_rep1_hg38_sort_dedup.bam - output: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam - log: RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.out, RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=6096, disk_mb=6392, disk_mib=6096, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam RES_ATAC/03-Deduplication/ATAC_D6_rep1_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam) && (samtools index RES_ATAC/04-NobiasedRegions/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.bam > RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.out) 2> RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep1_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 00:25:21 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.err deleted file mode 100644 index 300c777..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=8409, disk_mib=8020, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 05:02:41 2024] -localrule remove_biasedRegions: - input: RES_ATAC/03-Deduplication/ATAC_D6_rep2_hg38_sort_dedup.bam - output: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam - log: RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.out, RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=7630, disk_mb=8409, disk_mib=8020, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam RES_ATAC/03-Deduplication/ATAC_D6_rep2_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam) && (samtools index RES_ATAC/04-NobiasedRegions/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.bam > RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.out) 2> RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep2_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 05:16:23 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.err deleted file mode 100644 index 13bf7e0..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.err +++ /dev/null @@ -1,30 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=6410, disk_mb=6721, disk_mib=6410, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:06:50 2024] -localrule remove_biasedRegions: - input: RES_ATAC/03-Deduplication/ATAC_D6_rep3_hg38_sort_dedup.bam - output: RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam - log: RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.out, RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=ATAC_D6_rep3, REF=hg38 - resources: mem_mb=9537, mem_mib=6410, disk_mb=6721, disk_mib=6410, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam RES_ATAC/03-Deduplication/ATAC_D6_rep3_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam) && (samtools index RES_ATAC/04-NobiasedRegions/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.bam > RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.out) 2> RES_ATAC/04-NobiasedRegions/logs/ATAC_D6_rep3_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 10:17:10 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index e81959f..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4588, disk_mb=4810, disk_mib=4588, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:39:58 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=4588, disk_mb=4810, disk_mib=4588, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:48:06 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index d6eb724..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=2733, disk_mb=2865, disk_mib=2733, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:16:09 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=2733, disk_mb=2865, disk_mib=2733, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep1_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 21:20:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index 845b38c..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4831, disk_mb=5065, disk_mib=4831, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:41:00 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=4831, disk_mb=5065, disk_mib=4831, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:49:34 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index 7bab108..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=2573, disk_mb=2697, disk_mib=2573, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:15:10 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shCtrl_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=2573, disk_mb=2697, disk_mib=2573, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shCtrl_Rep2_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 22:19:25 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index e9e57ba..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=5459, disk_mb=5724, disk_mib=5459, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 15:11:52 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=5459, disk_mb=5724, disk_mib=5459, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Tue Aug 27 15:21:18 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 194a6d4..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=2780, disk_mb=2914, disk_mib=2780, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:43:07 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=2780, disk_mb=2914, disk_mib=2780, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep1_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 21:47:44 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index e1017bd..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4270, disk_mb=4477, disk_mib=4270, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:47:04 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=4270, disk_mb=4477, disk_mib=4270, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:54:34 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 3469839..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=2529, disk_mb=2651, disk_mib=2529, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 20:51:07 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=H3K27ac_shUbc9_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=2529, disk_mb=2651, disk_mib=2529, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/H3K27ac_shUbc9_Rep2_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 20:55:19 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index b3049ec..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3980, disk_mb=4173, disk_mib=3980, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 15:00:52 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=3980, disk_mb=4173, disk_mib=3980, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Tue Aug 27 15:08:10 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 0c77858..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=2076, disk_mb=2176, disk_mib=2076, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:01:06 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=2076, disk_mb=2176, disk_mib=2076, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep1_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 23:04:25 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index 0efe08d..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4552, disk_mb=4773, disk_mib=4552, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Aug 28 14:20:42 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=4552, disk_mb=4773, disk_mib=4552, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Aug 28 14:29:03 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index 31dc033..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=2930, disk_mb=3072, disk_mib=2930, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:58:42 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shCtrl_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=2930, disk_mb=3072, disk_mib=2930, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shCtrl_Rep2_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 11:03:31 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index 2da8723..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4550, disk_mb=4771, disk_mib=4550, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Aug 29 11:00:04 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=4550, disk_mb=4771, disk_mib=4550, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Aug 29 11:08:32 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index 3cf607f..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=2632, disk_mb=2759, disk_mib=2632, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:58:42 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=2632, disk_mb=2759, disk_mib=2632, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep1_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 11:03:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index 9a7d168..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4876, disk_mb=5112, disk_mib=4876, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Aug 29 11:00:06 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=4876, disk_mb=5112, disk_mib=4876, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Aug 29 11:09:05 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index 5fae6a4..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3361, disk_mb=3524, disk_mib=3361, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 10:59:48 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=INPUT_shUbc9_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=3361, disk_mb=3524, disk_mib=3361, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/INPUT_shUbc9_Rep2_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/INPUT_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Thu Sep 12 11:05:22 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err deleted file mode 100644 index b2a681d..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3829, disk_mb=4014, disk_mib=3829, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:33:53 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=3829, disk_mb=4014, disk_mib=3829, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep1_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:40:16 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err deleted file mode 100644 index 068746d..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3663, disk_mb=3840, disk_mib=3663, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:23:15 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=3663, disk_mb=3840, disk_mib=3663, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep1_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 21:29:11 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err deleted file mode 100644 index 9f313e7..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3500, disk_mb=3669, disk_mib=3500, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:38:55 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=3500, disk_mb=3669, disk_mib=3500, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep2_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Tue Aug 27 14:44:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err deleted file mode 100644 index 45aff0d..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3244, disk_mb=3401, disk_mib=3244, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 20:49:09 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shCtrl_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=3244, disk_mb=3401, disk_mib=3244, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shCtrl_Rep2_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 20:54:21 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err deleted file mode 100644 index 973218b..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3953, disk_mb=4144, disk_mib=3953, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Tue Aug 27 14:57:00 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=hg38 - resources: mem_mb=9537, mem_mib=3953, disk_mb=4144, disk_mib=3953, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep1_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Tue Aug 27 15:03:35 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err deleted file mode 100644 index e3dce91..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=3721, disk_mb=3901, disk_mib=3721, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:40:08 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep1, REF=mm10 - resources: mem_mb=9537, mem_mib=3721, disk_mb=3901, disk_mib=3721, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep1_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 22:46:07 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err deleted file mode 100644 index 8e4d845..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:385: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4809, disk_mb=5042, disk_mib=4809, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Aug 28 14:20:22 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_hg38_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=hg38 - resources: mem_mb=9537, mem_mib=4809, disk_mb=5042, disk_mib=4809, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_hg38_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep2_hg38_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Aug 28 14:28:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out deleted file mode 100644 index 0cfbf08..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out +++ /dev/null @@ -1 +0,0 @@ -2 diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err deleted file mode 100644 index cc7effb..0000000 --- a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=4612, disk_mb=4835, disk_mib=4612, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:36:05 2024] -localrule remove_biasedRegions: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_mm10_sort_dedup.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.err - jobid: 0 - reason: Forced execution - wildcards: SAMPLE=Klf4_shUbc9_Rep2, REF=mm10 - resources: mem_mb=9537, mem_mib=4612, disk_mb=4835, disk_mib=4612, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - (intersectBed -v -abam /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/03-Deduplication/Klf4_shUbc9_Rep2_mm10_sort_dedup.bam -b /pasteur/zeus/projets/p01/BioIT/Genomes/mm10_GRCm39_104/mm10-blacklist.v2.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam) && (samtools index /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.out) 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/logs/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.err - -Activating singularity image epeak.sif -[Wed Sep 11 22:43:33 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.err b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.err deleted file mode 100644 index b01318e..0000000 --- a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 23:11:09 2024] -localrule reproduciblePeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_IA.bed - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_IA.bed.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=H3K27ac_shCtrl, CONSENSUS_MOD=IA.bed - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_IA.bed >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_IA.bed.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_IA.bed >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_IA.bed.o 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 11 23:11:28 2024] -Error in rule reproduciblePeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_IA.bed - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_IA.bed.o (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_IA.bed >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_IA.bed.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_IA.bed >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_IA.bed.o 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.out b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=select.narrowPeak.err b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=select.narrowPeak.err deleted file mode 100644 index 9f4496a..0000000 --- a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=select.narrowPeak.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:22 2024] -localrule reproduciblePeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_select.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_select.narrowPeak.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=H3K27ac_shCtrl, CONSENSUS_MOD=select.narrowPeak - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_select.narrowPeak.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_select.narrowPeak.o 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:47 2024] -Error in rule reproduciblePeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_select.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_select.narrowPeak.o (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_select.narrowPeak.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shCtrl_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shCtrl_select.narrowPeak.o 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=select.narrowPeak.out b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=select.narrowPeak.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CONSENSUS_MOD=select.narrowPeak.err b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CONSENSUS_MOD=select.narrowPeak.err deleted file mode 100644 index d837738..0000000 --- a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CONSENSUS_MOD=select.narrowPeak.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:19 2024] -localrule reproduciblePeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_select.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_select.narrowPeak.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=H3K27ac_shUbc9, CONSENSUS_MOD=select.narrowPeak - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_select.narrowPeak.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_select.narrowPeak.o 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:37 2024] -Error in rule reproduciblePeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_select.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_select.narrowPeak.o (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_select.narrowPeak.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/H3K27ac_shUbc9_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/H3K27ac_shUbc9_select.narrowPeak.o 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CONSENSUS_MOD=select.narrowPeak.out b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CONSENSUS_MOD=select.narrowPeak.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CONSENSUS_MOD=select.narrowPeak.err b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CONSENSUS_MOD=select.narrowPeak.err deleted file mode 100644 index f3fa866..0000000 --- a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CONSENSUS_MOD=select.narrowPeak.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:22 2024] -localrule reproduciblePeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_select.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shCtrl_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_select.narrowPeak.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=Klf4_shCtrl, CONSENSUS_MOD=select.narrowPeak - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shCtrl_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_select.narrowPeak.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shCtrl_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_select.narrowPeak.o 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:46 2024] -Error in rule reproduciblePeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_select.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shCtrl_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_select.narrowPeak.o (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shCtrl_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_select.narrowPeak.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shCtrl_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shCtrl_select.narrowPeak.o 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CONSENSUS_MOD=select.narrowPeak.out b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CONSENSUS_MOD=select.narrowPeak.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CONSENSUS_MOD=select.narrowPeak.err b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CONSENSUS_MOD=select.narrowPeak.err deleted file mode 100644 index ac5d532..0000000 --- a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CONSENSUS_MOD=select.narrowPeak.err +++ /dev/null @@ -1,61 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 13:56:22 2024] -localrule reproduciblePeakAnnotation: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_select.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shUbc9_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_select.narrowPeak.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, IP_IDR=Klf4_shUbc9, CONSENSUS_MOD=select.narrowPeak - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shUbc9_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_select.narrowPeak.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shUbc9_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_select.narrowPeak.o 2>&1 - fi - - -Activating singularity image epeak.sif -[Wed Sep 4 13:56:47 2024] -Error in rule reproduciblePeakAnnotation: - jobid: 0 - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_select.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shUbc9_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_select.narrowPeak.o (check log file(s) for error details) - shell: - - set +o pipefail - - if [ "True" = "True" ] - then - sh workflow/scripts/annote_peaks.sh test/annotation/Mus_musculus.GRCm39.111.gtf test/annotation/Mus_musculus.Ensembl111.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shUbc9_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_select.narrowPeak.o 2>&1 - else - sh workflow/scripts/annote_peaks.sh config/annotation_config.txt /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_select.narrowPeak /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/Klf4_shUbc9_select.narrowPeak >/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/annotated_peaks/logs/Klf4_shUbc9_select.narrowPeak.o 2>&1 - fi - - - (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) - -Shutting down, this might take some time. -Exiting because a job execution failed. Look above for error message -Storing output in storage. -WorkflowError: -At least one job did not complete successfully. diff --git a/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CONSENSUS_MOD=select.narrowPeak.out b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CONSENSUS_MOD=select.narrowPeak.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.err b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.err deleted file mode 100644 index 3db34c6..0000000 --- a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.err +++ /dev/null @@ -1,35 +0,0 @@ -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 10:18:01 2024] -localrule select_peaks: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPRPool_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shCtrl_selected_peaks.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2, IP_IDR=H3K27ac_shCtrl - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - numPeaks_Rep=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak | cut -d' ' -f1) - numPeaks_PPR=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak | cut -d' ' -f1) - - if [ ${numPeaks_Rep} -gt ${numPeaks_PPR} ] ; then opTh=${numPeaks_Rep} ; - else opTh=${numPeaks_PPR} ; fi - - sort -k8nr,8nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPRPool_peaks.narrowPeak | head -n ${opTh} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_select.narrowPeak 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shCtrl_selected_peaks.o - - -Activating singularity image epeak.sif -[Wed Sep 4 10:18:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.out b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.err b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.err deleted file mode 100644 index 3eb9143..0000000 --- a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 10:57:24 2024] -localrule select_peaks: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPRPool_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shUbc9_selected_peaks.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2, IP_IDR=H3K27ac_shUbc9 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - numPeaks_Rep=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak | cut -d' ' -f1) - numPeaks_PPR=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/H3K27ac_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak | cut -d' ' -f1) - - if [ ${numPeaks_Rep} -gt ${numPeaks_PPR} ] ; then opTh=${numPeaks_Rep} ; - else opTh=${numPeaks_PPR} ; fi - - sort -k8nr,8nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPRPool_peaks.narrowPeak | head -n ${opTh} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_select.narrowPeak 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/H3K27ac_shUbc9_selected_peaks.o - - -Activating singularity image epeak.sif -[Wed Sep 4 10:57:26 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.out b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.out deleted file mode 100644 index 9a099f9..0000000 --- a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.out +++ /dev/null @@ -1 +0,0 @@ -['shCtrl', 'shUbc9'] diff --git a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.err b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.err deleted file mode 100644 index 1f62e64..0000000 --- a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 10:57:30 2024] -localrule select_peaks: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPRPool_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shCtrl_selected_peaks.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2, IP_IDR=Klf4_shCtrl - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - numPeaks_Rep=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak | cut -d' ' -f1) - numPeaks_PPR=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shCtrl_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak | cut -d' ' -f1) - - if [ ${numPeaks_Rep} -gt ${numPeaks_PPR} ] ; then opTh=${numPeaks_Rep} ; - else opTh=${numPeaks_PPR} ; fi - - sort -k8nr,8nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPRPool_peaks.narrowPeak | head -n ${opTh} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_select.narrowPeak 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shCtrl_selected_peaks.o - - -Activating singularity image epeak.sif -[Wed Sep 4 10:57:31 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.out b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.out deleted file mode 100644 index 9a099f9..0000000 --- a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.out +++ /dev/null @@ -1 +0,0 @@ -['shCtrl', 'shUbc9'] diff --git a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.err b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.err deleted file mode 100644 index 81b491a..0000000 --- a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.err +++ /dev/null @@ -1,41 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 4 10:59:30 2024] -localrule select_peaks: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPRPool_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_select.narrowPeak - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shUbc9_selected_peaks.o - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2, IP_IDR=Klf4_shUbc9 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - set +o pipefail - - numPeaks_Rep=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_Rep1vsRep2_mm10_narrow_idr0.05.narrowPeak | cut -d' ' -f1) - numPeaks_PPR=$(wc -l /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/07-IDR/macs2_narrow/Klf4_shUbc9_PPR1vsPPR2_mm10_narrow_idr0.05.narrowPeak | cut -d' ' -f1) - - if [ ${numPeaks_Rep} -gt ${numPeaks_PPR} ] ; then opTh=${numPeaks_Rep} ; - else opTh=${numPeaks_PPR} ; fi - - sort -k8nr,8nr /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPRPool_peaks.narrowPeak | head -n ${opTh} > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_select.narrowPeak 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/Klf4_shUbc9_selected_peaks.o - - -Activating singularity image epeak.sif -[Wed Sep 4 10:59:31 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.out b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.out deleted file mode 100644 index 9a099f9..0000000 --- a/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.out +++ /dev/null @@ -1 +0,0 @@ -['shCtrl', 'shUbc9'] diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.err b/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.err deleted file mode 100644 index cbbfd12..0000000 --- a/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=2547, disk_mb=2670, disk_mib=2547, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:21:09 2024] -localrule spp: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_phantom.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_spp.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shCtrl_Rep1_phantom.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shCtrl_Rep1_phantom.err - jobid: 0 - reason: Forced execution - wildcards: ALL=H3K27ac_shCtrl_Rep1 - resources: mem_mb=19073, mem_mib=2547, disk_mb=2670, disk_mib=2547, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - Rscript workflow/scripts/run_spp.R -c=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -odir=. -savp=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_phantom.pdf -out=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_spp.out -tmpdir=$TMPDIR > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shCtrl_Rep1_phantom.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shCtrl_Rep1_phantom.err - -Activating singularity image epeak.sif -[Wed Sep 11 21:52:38 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.out b/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.err b/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.err deleted file mode 100644 index e9b668a..0000000 --- a/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=2394, disk_mb=2510, disk_mib=2394, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:20:11 2024] -localrule spp: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_phantom.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_spp.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shCtrl_Rep2_phantom.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shCtrl_Rep2_phantom.err - jobid: 0 - reason: Forced execution - wildcards: ALL=H3K27ac_shCtrl_Rep2 - resources: mem_mb=19073, mem_mib=2394, disk_mb=2510, disk_mib=2394, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - Rscript workflow/scripts/run_spp.R -c=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -odir=. -savp=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_phantom.pdf -out=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_spp.out -tmpdir=$TMPDIR > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shCtrl_Rep2_phantom.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shCtrl_Rep2_phantom.err - -Activating singularity image epeak.sif -[Wed Sep 11 22:42:31 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.out b/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.err b/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.err deleted file mode 100644 index 26c59de..0000000 --- a/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=2589, disk_mb=2714, disk_mib=2589, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:48:15 2024] -localrule spp: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_phantom.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_spp.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shUbc9_Rep1_phantom.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shUbc9_Rep1_phantom.err - jobid: 0 - reason: Forced execution - wildcards: ALL=H3K27ac_shUbc9_Rep1 - resources: mem_mb=19073, mem_mib=2589, disk_mb=2714, disk_mib=2589, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - Rscript workflow/scripts/run_spp.R -c=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -odir=. -savp=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_phantom.pdf -out=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_spp.out -tmpdir=$TMPDIR > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shUbc9_Rep1_phantom.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shUbc9_Rep1_phantom.err - -Activating singularity image epeak.sif -[Wed Sep 11 22:12:15 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.out b/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.err b/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.err deleted file mode 100644 index d744b28..0000000 --- a/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=2356, disk_mb=2470, disk_mib=2356, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 20:56:05 2024] -localrule spp: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_phantom.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_spp.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shUbc9_Rep2_phantom.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shUbc9_Rep2_phantom.err - jobid: 0 - reason: Forced execution - wildcards: ALL=H3K27ac_shUbc9_Rep2 - resources: mem_mb=19073, mem_mib=2356, disk_mb=2470, disk_mib=2356, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - Rscript workflow/scripts/run_spp.R -c=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -odir=. -savp=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_phantom.pdf -out=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/H3K27ac_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_spp.out -tmpdir=$TMPDIR > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shUbc9_Rep2_phantom.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/H3K27ac_shUbc9_Rep2_phantom.err - -Activating singularity image epeak.sif -[Wed Sep 11 21:19:55 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.out b/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.err b/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.err deleted file mode 100644 index 901a6e0..0000000 --- a/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=3400, disk_mb=3565, disk_mib=3400, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 21:30:11 2024] -localrule spp: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_phantom.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_spp.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shCtrl_Rep1_phantom.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shCtrl_Rep1_phantom.err - jobid: 0 - reason: Forced execution - wildcards: ALL=Klf4_shCtrl_Rep1 - resources: mem_mb=19073, mem_mib=3400, disk_mb=3565, disk_mib=3400, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - Rscript workflow/scripts/run_spp.R -c=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions.bam -odir=. -savp=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_phantom.pdf -out=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shCtrl_Rep1_mm10_sort_dedup_biasedRegions_spp.out -tmpdir=$TMPDIR > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shCtrl_Rep1_phantom.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shCtrl_Rep1_phantom.err - -Activating singularity image epeak.sif -[Wed Sep 11 22:20:25 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.out b/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.err b/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.err deleted file mode 100644 index 0c38c3d..0000000 --- a/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=3018, disk_mb=3164, disk_mib=3018, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 20:55:05 2024] -localrule spp: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_phantom.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_spp.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shCtrl_Rep2_phantom.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shCtrl_Rep2_phantom.err - jobid: 0 - reason: Forced execution - wildcards: ALL=Klf4_shCtrl_Rep2 - resources: mem_mb=19073, mem_mib=3018, disk_mb=3164, disk_mib=3018, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - Rscript workflow/scripts/run_spp.R -c=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions.bam -odir=. -savp=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_phantom.pdf -out=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shCtrl_Rep2_mm10_sort_dedup_biasedRegions_spp.out -tmpdir=$TMPDIR > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shCtrl_Rep2_phantom.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shCtrl_Rep2_phantom.err - -Activating singularity image epeak.sif -[Wed Sep 11 21:29:14 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.out b/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.err b/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.err deleted file mode 100644 index 547cf86..0000000 --- a/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=3461, disk_mb=3629, disk_mib=3461, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:47:10 2024] -localrule spp: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_phantom.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_spp.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shUbc9_Rep1_phantom.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shUbc9_Rep1_phantom.err - jobid: 0 - reason: Forced execution - wildcards: ALL=Klf4_shUbc9_Rep1 - resources: mem_mb=19073, mem_mib=3461, disk_mb=3629, disk_mib=3461, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - Rscript workflow/scripts/run_spp.R -c=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions.bam -odir=. -savp=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_phantom.pdf -out=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shUbc9_Rep1_mm10_sort_dedup_biasedRegions_spp.out -tmpdir=$TMPDIR > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shUbc9_Rep1_phantom.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shUbc9_Rep1_phantom.err - -Activating singularity image epeak.sif -[Wed Sep 11 23:25:39 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.out b/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.err b/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.err deleted file mode 100644 index e75d0f4..0000000 --- a/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.err +++ /dev/null @@ -1,32 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=19073, mem_mib=4287, disk_mb=4495, disk_mib=4287, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Wed Sep 11 22:44:14 2024] -localrule spp: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_phantom.pdf, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_spp.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shUbc9_Rep2_phantom.out, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shUbc9_Rep2_phantom.err - jobid: 0 - reason: Forced execution - wildcards: ALL=Klf4_shUbc9_Rep2 - resources: mem_mb=19073, mem_mib=4287, disk_mb=4495, disk_mib=4287, tmpdir=/pasteur/appa/scratch/rlegendr, mem=20G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - Rscript workflow/scripts/run_spp.R -c=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/04-NobiasedRegions/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions.bam -odir=. -savp=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_phantom.pdf -out=/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/Klf4_shUbc9_Rep2_mm10_sort_dedup_biasedRegions_spp.out -tmpdir=$TMPDIR > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shUbc9_Rep2_phantom.out 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/05-QC/PhantomPeakQualTools/logs/Klf4_shUbc9_Rep2_phantom.err - -Activating singularity image epeak.sif -[Wed Sep 11 23:34:24 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.out b/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/stats_IA/stats_IA_unique.err b/logs/slurm/stats_IA/stats_IA_unique.err deleted file mode 100644 index 6f4f6d4..0000000 --- a/logs/slurm/stats_IA/stats_IA_unique.err +++ /dev/null @@ -1,27 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:15:50 2024] -localrule stats_IA: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_IA.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_IA.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_IA.bed - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/IA_metrics.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/logs/IA_metrics.out - jobid: 0 - reason: Forced execution - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -[Thu Sep 12 11:15:51 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/stats_IA/stats_IA_unique.out b/logs/slurm/stats_IA/stats_IA_unique.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=genrich.MOD=narrow.FORM=narrow.err b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=genrich.MOD=narrow.FORM=narrow.err deleted file mode 100644 index 0ad8e7a..0000000 --- a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=genrich.MOD=narrow.FORM=narrow.err +++ /dev/null @@ -1,26 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:15:56 2024] -localrule stats_peakCalling: - input: RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/genrich_narrow/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/genrich_narrow_narrow_Peaks_metrics_mqc.out - log: RES_ATAC/06-PeakCalling/genrich_narrow/narrow_narrow_Peaks_metrics.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -[Thu Sep 12 12:15:56 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=genrich.MOD=narrow.FORM=narrow.out b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=genrich.MOD=narrow.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err deleted file mode 100644 index 39691c7..0000000 --- a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err +++ /dev/null @@ -1,26 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:11:02 2024] -localrule stats_peakCalling: - input: RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/lanceOtron_narrow/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/lanceOtron_narrow_narrow_Peaks_metrics_mqc.out - log: RES_ATAC/06-PeakCalling/lanceOtron_narrow/narrow_narrow_Peaks_metrics.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -[Thu Sep 12 12:11:04 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=lanceOtron.MOD=narrow.FORM=narrow.out b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=lanceOtron.MOD=narrow.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs2.MOD=narrow.err b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs2.MOD=narrow.err deleted file mode 100644 index 0cfefe8..0000000 --- a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs2.MOD=narrow.err +++ /dev/null @@ -1,28 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=9698, disk_mib=9249, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:14:45 2024] -localrule stats_peakCalling: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_Rep2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_Rep2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR2.2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_SPR1.2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR1.2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_SPR2.2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR2.2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_SPR1.2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR1.2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_SPR2.2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPR1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPR2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPR1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR1_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPR2_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shCtrl_PPRPool_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/H3K27ac_shUbc9_PPRPool_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shCtrl_PPRPool_peaks.narrowPeak, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/Klf4_shUbc9_PPRPool_peaks.narrowPeak - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/macs2_narrow_Peaks_metrics_mqc.out - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/06-PeakCalling/macs2_narrow/narrow_Peaks_metrics.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2, MOD=narrow - resources: mem_mb=9537, mem_mib=7630, disk_mb=9698, disk_mib=9249, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -[Thu Sep 12 11:15:07 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs2.MOD=narrow.out b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs2.MOD=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err deleted file mode 100644 index 4094277..0000000 --- a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err +++ /dev/null @@ -1,26 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:42:53 2024] -localrule stats_peakCalling: - input: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D0_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep1_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6F_rep2_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep3_peaks.narrowPeak, RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/ATAC_D6_rep2_peaks.narrowPeak - output: RES_ATAC/macs3_CallPeak_noModel_narrow_Peaks_metrics_mqc.out - log: RES_ATAC/06-PeakCalling/macs3_CallPeak_noModel/noModel_narrow_Peaks_metrics.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, FORM=narrow - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - -[Thu Sep 12 11:42:55 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.out b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=genrich.MOD=narrow.MARK=ATAC.err b/logs/slurm/union_peaks/union_peaks_CALLER=genrich.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index 5d9b4cf..0000000 --- a/logs/slurm/union_peaks/union_peaks_CALLER=genrich.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:26:45 2024] -localrule union_peaks: - input: RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed - output: RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed - log: RES_ATAC/09-CountMatrix/genrich_narrow/logs/ATAC_Optimal_selected_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=genrich, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - cat RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed RES_ATAC/08-ReproduciblePeaks/genrich_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed | sort -k1,1 -k2,2n - > RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed_SORT.bed - - bedtools merge -i RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed_SORT.bed > RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed 2> RES_ATAC/09-CountMatrix/genrich_narrow/logs/ATAC_Optimal_selected_peaks.out - - rm RES_ATAC/09-CountMatrix/genrich_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed_SORT.bed - - -Activating singularity image epeak.sif -[Thu Sep 12 12:26:46 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=genrich.MOD=narrow.MARK=ATAC.out b/logs/slurm/union_peaks/union_peaks_CALLER=genrich.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err b/logs/slurm/union_peaks/union_peaks_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err deleted file mode 100644 index 7cb00d5..0000000 --- a/logs/slurm/union_peaks/union_peaks_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 12:58:48 2024] -localrule union_peaks: - input: RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed - output: RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed - log: RES_ATAC/09-CountMatrix/lanceOtron_narrow/logs/ATAC_Optimal_selected_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=lanceOtron, MOD=narrow, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - cat RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D0_DONE_optimal.bed RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6_DONE_optimal.bed RES_ATAC/08-ReproduciblePeaks/lanceOtron_narrow/Chipr_narrow/ATAC_D6F_DONE_optimal.bed | sort -k1,1 -k2,2n - > RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed_SORT.bed - - bedtools merge -i RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed_SORT.bed > RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed 2> RES_ATAC/09-CountMatrix/lanceOtron_narrow/logs/ATAC_Optimal_selected_peaks.out - - rm RES_ATAC/09-CountMatrix/lanceOtron_narrow/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed_SORT.bed - - -Activating singularity image epeak.sif -[Thu Sep 12 12:58:49 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out b/logs/slurm/union_peaks/union_peaks_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=H3K27ac.err b/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=H3K27ac.err deleted file mode 100644 index 06cd730..0000000 --- a/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=H3K27ac.err +++ /dev/null @@ -1,38 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:11:54 2024] -localrule union_peaks: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_IA.bed - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/H3K27ac_Optimal_selected_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=H3K27ac - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shCtrl_IA.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/H3K27ac_shUbc9_IA.bed | sort -k1,1 -k2,2n - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed_SORT.bed - - bedtools merge -i /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed_SORT.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/H3K27ac_Optimal_selected_peaks.out - - rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/H3K27ac_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed_SORT.bed - - -Activating singularity image epeak.sif -[Thu Sep 12 11:11:56 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=H3K27ac.out b/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=H3K27ac.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=Klf4.err b/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=Klf4.err deleted file mode 100644 index d41e811..0000000 --- a/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=Klf4.err +++ /dev/null @@ -1,38 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.' - POOL = "[A-Za-z-_0-9]+_PPRPool", -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - # if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:15:50 2024] -localrule union_peaks: - input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_IA.bed, /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_IA.bed - output: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed - log: /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/Klf4_Optimal_selected_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs2_narrow, MARK=Klf4 - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - - cat /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shCtrl_IA.bed /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/08-ReproduciblePeaks/macs2_narrow/Klf4_shUbc9_IA.bed | sort -k1,1 -k2,2n - > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed_SORT.bed - - bedtools merge -i /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed_SORT.bed > /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed 2> /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/logs/Klf4_Optimal_selected_peaks.out - - rm /pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/RES_CHIP/09-CountMatrix/macs2_narrow/Klf4_shCtrlushUbc9_mm10.optimal.Peak_overlap.bed_SORT.bed - - -Activating singularity image epeak.sif -[Thu Sep 12 11:15:52 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=Klf4.out b/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=Klf4.out deleted file mode 100644 index e69de29..0000000 diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err b/logs/slurm/union_peaks/union_peaks_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err deleted file mode 100644 index e5d5c5c..0000000 --- a/logs/slurm/union_peaks/union_peaks_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err +++ /dev/null @@ -1,35 +0,0 @@ -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/' - rep.append(sample.split("_")[2]) -/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/' - #if spikes, read json file -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 1 (use --cores to define parallelism) -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, threads=1 -Select jobs to execute... -Execute 1 jobs... - -[Thu Sep 12 11:57:54 2024] -localrule union_peaks: - input: RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_optimal.bed, RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_optimal.bed - output: RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed - log: RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/logs/ATAC_Optimal_selected_peaks.out - jobid: 0 - reason: Forced execution - wildcards: CALLER=macs3_CallPeak, MOD=noModel, MARK=ATAC - resources: mem_mb=9537, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit - - - cat RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D0_DONE_optimal.bed RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6_DONE_optimal.bed RES_ATAC/08-ReproduciblePeaks/macs3_CallPeak_noModel/Chipr_narrow/ATAC_D6F_DONE_optimal.bed | sort -k1,1 -k2,2n - > RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed_SORT.bed - - bedtools merge -i RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed_SORT.bed > RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed 2> RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/logs/ATAC_Optimal_selected_peaks.out - - rm RES_ATAC/09-CountMatrix/macs3_CallPeak_noModel/ATAC_D0uD6uD6F_hg38.optimal.Peak_overlap.bed_SORT.bed - - -Activating singularity image epeak.sif -[Thu Sep 12 11:57:55 2024] -Finished job 0. -1 of 1 steps (100%) done -Storing output in storage. diff --git a/logs/slurm/union_peaks/union_peaks_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out b/logs/slurm/union_peaks/union_peaks_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out deleted file mode 100644 index e69de29..0000000 diff --git a/singularity/.gitkeep b/singularity/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/singularity/epeak.def b/singularity/epeak.def deleted file mode 100644 index ff24f8e..0000000 --- a/singularity/epeak.def +++ /dev/null @@ -1,131 +0,0 @@ -BootStrap: docker - -From: ubuntu:20.04 - - -%labels - - Authors Adrien Pain, Rachel Legendre - package.name ePeak - package.version latest - package.homepage https://gitlab.pasteur.fr/hub/ePeak - package.license GPLv3 - -%environment - ## export all variables - export LC_ALL=C.UTF-8 - export LANG=C.UTF-8 - export PATH=$PATH:/usr/local/lib/ - export DEBIAN_FRONTEND=noninteractive - -%post - -# echo "deb http://archive.ubuntu.com/ubuntu focal main universe" >> /etc/apt/sources.list -# echo "deb http://archive.ubuntu.com/ubuntu focal-security main universe" >> /etc/apt/sources.list -# echo "deb http://archive.ubuntu.com/ubuntu focal-updates main universe" >> /etc/apt/sources.list - - apt update -y - apt upgrade -y - - export DEBIAN_FRONTEND=noninteractive - - apt -y install locales - locale-gen en_US.UTF-8 - - - apt install -y python3-pip curl unzip wget git gzip tar - #apt install -y python3-dev python3-setuptools - pip3 install numpy matplotlib scipy - pip3 install pysam cutadapt macs2 - pip3 install multiqc - pip3 install deeptools - - echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" >> /etc/apt/sources.list - apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 - - apt update -y - apt upgrade -y - - apt install -y fastqc bowtie2 picard-tools subread bedtools r-base - - apt install -y gcc make libbz2-dev zlib1g-dev libncurses5-dev libncursesw5-dev liblzma-dev libfontconfig1-dev - apt install -y samtools - - cd /opt - wget https://github.com/nboley/idr/archive/2.0.3.zip - unzip 2.0.3.zip - cd idr-2.0.3/ - python3 setup.py install - - apt install -y aptitude libcurl4-openssl-dev libxml2-dev libssl-dev - apt install -y libboost-dev - # install gawk for spp package - apt install -y gawk - ln -fs /usr/bin/gawk /usr/bin/awk - - wget https://github.com/hms-dbmi/spp/archive/1.15.2.tar.gz - - echo 'install.packages("snow", repos="http://cran.us.r-project.org")' > spp.txt - echo 'install.packages("snowfall", repos="http://cran.us.r-project.org")' >> spp.txt - echo 'install.packages("bitops", repos="http://cran.us.r-project.org")' >> spp.txt - echo 'install.packages("caTools", repos="http://cran.us.r-project.org")' >> spp.txt - echo 'install.packages("RCurl", repos="http://cran.us.r-project.org")' >> spp.txt - echo 'install.packages("Rcpp", repos="http://cran.us.r-project.org")' >> spp.txt - echo 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' >> spp.txt - echo 'BiocManager::install()' >> spp.txt - echo 'BiocManager::install("GenomeInfoDb",suppressUpdates=TRUE)' >> spp.txt - echo 'BiocManager::install("GenomicRanges",suppressUpdates=TRUE)' >> spp.txt - echo 'BiocManager::install("Rsamtools",suppressUpdates=TRUE)' >> spp.txt - echo 'install.packages("./1.15.2.tar.gz")' >> spp.txt - Rscript spp.txt - - apt install -y build-essential libcurl4-gnutls-dev #for devtools package - cd /opt - #ln -s /bin/gzip /usr/bin/gzip - #ln -s /bin/tar /usr/bin/tar - export TAR="/bin/tar" - - echo "LC_ALL=en_US.UTF-8" >> /etc/environment - echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen - echo "LANG=en_US.UTF-8" > /etc/locale.conf - - apt -y install locales - locale-gen en_US.UTF-8 - - apt install -y pandoc - apt update -y - apt install -y pandoc-citeproc - - - #echo 'install.packages("colorspace")' > chipflowr.txt - #echo 'install.packages("viridisLite")' >> chipflowr.txt - echo 'install.packages("devtools", repos="http://cran.us.r-project.org")' > chipflowr.txt - echo 'library(devtools)' >> chipflowr.txt - echo 'install.packages("webshot", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'install.packages("highr", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'install.packages("xfun", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'install.packages("markdown", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'install.packages("rmarkdown", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'install.packages("knitr", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'install.packages("base64enc", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'install.packages("matrixStats", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'install.packages("DelayedArray", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'install.packages("tinytex", repos="http://cran.us.r-project.org")' >> chipflowr.txt - echo 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' >> chipflowr.txt - echo 'BiocManager::install()' >> chipflowr.txt - echo 'BiocManager::install("limma")' >> chipflowr.txt - echo 'BiocManager::install("Biobase")' >> chipflowr.txt - echo 'BiocManager::install("locfit")' >> chipflowr.txt - echo 'BiocManager::install("genefilter")' >> chipflowr.txt - echo 'BiocManager::install("RcppArmadillo")' >> chipflowr.txt - echo 'devtools::install_gitlab(repo="hub/chipflowr", host="gitlab.pasteur.fr", build_vignettes=TRUE)' >> chipflowr.txt - Rscript chipflowr.txt - - - - - - - - - -- GitLab