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
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 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
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-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
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-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
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-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 
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-- 
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