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 be94c452804a62d594021c1482bd3d02ef71cbd3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0bdeae9a71d468155bca28c3a0777bee0462e837..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 44c270629dc38a5a823734e6654d659d3bc1d2ed..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 4c0b491aad41c52aff043f540d88d507b7390688..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7c6c3dc6224268454bf9555e22af2f17a26c8077..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 81170c98897427a8f50f44bf2ff65edc80ca2359..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3d44b623c7194934feaa25b3e0c86f075398ef63..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b31b25f73b692fafee6ab1190d1d2964e0b3fdcc..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7a9a33f97ccae8eb948539b3f6d23f18942a9f82..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3c40126270c2dcac031c7cfd876db13c50f1f14e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ef4ec036c11cc0afd790297d29ae71b76984b19e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 dc8c82c4777fc60ed8fcefbf3b71ff5b0b727f9e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 1a45c1b210cf5bd22a17bd179ebc99fbbc74b8df..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ecd0027c2c64ca01fc0e9acfe4a6f96b7813937d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a94cff3009bbb7d2cd30d9872e7915773c4a14e7..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 739409dedc67de2fbd828874dbecfb1c8976a329..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b3988660e2a3e9c4a5424e7cd044a90501adca93..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 dffd4c230fd4449fc7aaa7d0460d54a8fdd93e72..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c62a8e5245fb62a6ed417cf1ef13c49079a777b5..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 24bee8ca4143c60e9d89e201613826a15dd00509..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 1eb284c60390cf35ad55782a62a57fbe1b0c2e78..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 7c2021c523f91cc1c10ad83eabc869a4ff5c9375..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 749020cc89d47969216dae7dab784c5e8f731649..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 aeb4f7e7d0d449651bd419ea6bf6a66398e4271d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 40ef0e360f7e02e74efebf4606a84742d0c5459b..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 9c0ff81fae15af2694bad74513669874ef7a231e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a4799c2e9e5dc318b9841e5c98dd7f8a383ec353..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 70ab6531db1a9cd6d9fe67a3693768bc5a9c6b41..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e3e0d06bf92780118d5df5c978c7a973127e8d57..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 54f58242cafdfb1962c1ed5e4115e077a5d99736..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ee0befb55b2096b590cb8718a3fd8ef8968cc79b..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 04109dd0ddbba36a67922e13d7e2dc79e15ba9e5..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 01d3a745ca569549fea3c5479827c0b9ba844af1..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 d1377ff7366ee348a1cbe17c5a8fd1ff3459c759..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a1430a610d81ceed38bb014274f52982d0612da3..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 a2082f6588d254806207b2c75fadaa495aed8ce3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c1e6fe1a8ebcf4c9e060d78872b099557d79805e..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 9aa2bda875d5f97db72b9c636b9b303e098ff91e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0b9d8f78eb709c3d963ef6f752d7e367c2132e0e..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 a5b0a5cb80885bed498af256aa3624b062b7e9f8..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e9276e832524fdd4a8fd6731c21bc39b99a3db58..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 ba14d083d5d09aacff5a20eab01cf470ce68b0fe..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c0fcf6bba6bfb66f5c214c65547ea4230118e453..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0dcfcdc884772afd1d5ecdb519819863630653bf..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 bca35879e4b978c22bf1edee784596c4adc76b0c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 1e9578090e0e9253427c65d886f7f5e14d5f15e0..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d13adcbea89dae91bae2508762f3cd124fe34bf3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 79a4068c56c167203bdf22609b4775a73dfe0c3c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a090b890b3f75009d16039892a02d15633d0bd61..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 980b23825f85ca0c5f0109d7cb7505634d4a51be..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 1265c4f6c120918dbb4839a2419939f19f82ee9b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7bf832896f586625f193bbfde29089d8b1a5a937..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 44b6315e89dbb1cee3c5ca0ac3edfaf936a67916..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 65fb646f87a66bd9d56bc840f336e2688b2b8abf..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 556c28effdc5cd3c0f04b06caddba2ba636bd21b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 85a32aa4dea925794af22ab9aa403e4d4c8fbf3d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e7a7aec9c1b9ab436642bcfe8408888fc41ee6e0..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c899ad9d6fc628c58067dc70cdaad12071605bf7..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 8da4050524bf841806d8f592af6920d5bb8bcc82..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 037c9946f7bb1f2d996c17a2147cc4af8c05192a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 46b0a6ab36f8558e61035e2c45c1c46eb9a71c17..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 020390761e4c1d3cdf0b52aa9793828f273526a0..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ed0f7a40cd50efdb08fb0c39aed8b34b566f0960..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a0509331f5b6ec36427447ac6bfafbb8f20bbbd3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 014fb2e7721d4aabbbef126e97d9dede935d0c57..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a37d98785ad0625c234be2fb5e5b675418ae5a3f..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 8934a2591ca5c72e19cf5bc71a1b9323c6739559..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6370f5c6675efa17d38590613eb0622771ff28ad..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 ffa9d68b5343d156c33569f3d61e8c6d1b5f057a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 87deb993ee7b0db5e7e75502a71b5fabda20b8f6..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 9e5d46b338215d09254cfbf84141690b74b88790..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6874e621cb8dba75c256c6ed52bf93050cb5a610..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 9c2bc1ef98440cb4d40fe6bffd548e4b2e9e9b8b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ecfc91dfc0c1cb76ed36b38fc2839ba17872ae66..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 34e7e8806757791facc54c14307ced4535b7b2a4..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7de24c574c49bb75ee8d1298aa543857934527a0..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 cdbfbec62a9f3d8400fbb0d8f24f9ac3d2cd6f10..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 93f316d7452478aaf1b9af1f89b6b3f1b22190ff..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 789a431514cd255b48fcb2b51252ced5eb314b33..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d09dbc1d8846e136b712d51cb409469a314ecf43..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 1ba52f266da4bc731e59274f62478b847ea17f71..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ff937bda09b15a76d3332d6392a6e336f00bb09f..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 3e0c3c0ca670ffb12243527ea80fb50bbc6f642e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 339905dee490e9344eb1a8c8319ad27e56c2422a..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 d5795f91e0164ff86a80e3d92ba590ffc1f1fec3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b2f467cc63b4aae2acf2a0f5b75a1a7abbfacbcb..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 33d93c71af15cd36745c07a8eb41096dec95e8da..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ad47acd4e85ea5b27117dec0cf35456af2c7d337..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 27dbdaf26cb4fabc9acce3e26981d49efd60e83a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 49bf0d3c162af151223b87d9b8bfcd8a750db92e..0000000000000000000000000000000000000000
--- 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 499c5fbff433111055934f6484f3161d5c629cf1..0000000000000000000000000000000000000000
--- 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 0a87d0fe0cd765d9b841add7d920e30d8ca07236..0000000000000000000000000000000000000000
--- 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 ae9ce67d4847a5d540c84f56072102dae409abe9..0000000000000000000000000000000000000000
--- 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 c6d01f96f6d4886dc66b152b887f6979f7519300..0000000000000000000000000000000000000000
--- 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 f2f0e3ce03164cbb41c5489ffceff1f90540a9bb..0000000000000000000000000000000000000000
--- 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 da4e2488c57d1afec99d2a390d10e89698014a76..0000000000000000000000000000000000000000
--- 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 36d347b7fa4ccdf1e975487a76511c53fd5bb75c..0000000000000000000000000000000000000000
--- 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 6865148d2c4eb5b8ed77035d4e52ea2a1cbe3261..0000000000000000000000000000000000000000
--- 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 fbdbf443dbbfd3c0e58b85b1d8e1f961b5e4624d..0000000000000000000000000000000000000000
--- 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 3a595a54ff1396504fe9010190a9201c3ce2a10f..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a17840c726f6ec1e3b02c70a5f9bc30ff59c9d0a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 25f003f8ac98b73c8767e7798fdd1fdaf51e56e3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b5f092408d316ba5ae25ad09cebb96043f2294bb..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c2a8383f4310172121f1c04e4829efc241843171..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 cfb00a34633ce733563a4fe1450a24780e723afc..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b14935a3c7f266f789830f8b1bc50ed316aee397..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b3df6d29cbf3634180f5c714595c206e0b0acf35..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 996d22116dc4e323b3a215fb246cec61316e7107..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 87aedbcf73215ac3c994ce01d34cc86cc9df3871..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5c68c87963390f877f82a4281743a58f3b188dfd..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 4ce04d8dc305e18b5472e22af4bd3ca9bba4f10f..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 11e91ee2f3bcef9755549b81b10fe5950e5c31d3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0ca8cb698d7e75537b3301195824064cb16dc2d7..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 498546d42366920ee25f623de85418cd2d368b1c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 40d59f6772967dc74531623acd4d8abeee550930..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9f69168f5c1f5d1491888d70700181a62f259f85..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b06a948e4ccd8b064ee1891dd3bec78c209286f4..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6980cbea13d4a50600f53c3711b0738704d63f3b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6fcf97fd23d54e8f0ec536061b04ac68f5815af8..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 49561769e2edc4dcdbe89817209a4833b52c4291..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e234d3a25a3aaa4b7d93f6b1a39928b8c4145929..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e99c02988b98fdebe5daaace10a1cdf85f56dcbd..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5d08c702737a1a5ac2f74f8c6c1c4ba9da5d71b3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b2fd2d05178f075638866e8bed1c01322369a8db..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d48125f389a0275cdde85124fa9744d8b3b14e95..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6f49fdcc49d9b16f85394b89b06b2d6aa33f2681..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 4b2bb0e25d80b3dc926e75433351b9474d44eb8d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 de871123e6af5ef527ef356e2717732f95772916..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 adc6fafa965af8f3c1df43ed9b097f1d855e394d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 78970cd81730dbeed0e8ff98d4c6c0044808c5e0..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 034d530650abecc43549c8f82957b5e30108e479..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 156dfc068e2bcf6a8652eeb822cb031ad46f331c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9bb5a4fd35e7766f71e02e05c325ac6a34a881ac..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3ad593a5ae95a7f039cf50c9b905a3e3d25a8d3b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ce5e5a61f9bb6d9369a07777a3485e273dc3d46d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 db3f12b54bba2d4ef172f65fd84f6fcf5e3d20da..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a328aaa85fcc689b220ff56b667f916b437992d5..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 81d445b30f9583209f531d27d891985f4bc6c06c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 651a396071c477488cd71b956c3e41763c641bb4..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 94105abaa67dda7d7de56e72aeadf99fbbc6f2bd..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 08b4a0c28512ae12db35b37d9dde07002bc6fdd4..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e6e438aace1e6d51b1f0392e5db8c1357e759998..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5dc8655279766bdded097e36d3bba7d5f7d17980..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5399acbbe8f27432de8a7d7190860471d103063b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 1dc12ee936619f115f2b29822a73b2658a19530a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f56337e570d9a673c911c918d603385cd9cf0f0e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9a1557869db6deae5d731b3ef580c4882c15d314..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5884304cff04f64f02fb9b1531b6820f3c70d59c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 36eae4c233dc37450329b1ce3df879353ba10f11..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e2a51664f721444d519f4edbaf6ec93c7012c0b8..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2e601c1ff745bd4c00df76e0da21596675a7b777..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c7dca8502ad003b01e1fbd5dd64d2589c6bf46a2..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a44ab04e3504fb202a93d20c679bac349a901f48..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 009b83055392b85c1dbb0167dc7280721af2b2e7..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 8445e80502c03f0f6fd6a8696da9cdb969c7209e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2169de36516862394453e0fcb25db4486d8cebf4..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ebea0418cfecb5c5fe067ddbb7ada410201c78e4..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 806416deeeb0806fd0991bc74febcc9295b33b7b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7d24ea336858c9f2a6480e72cfa77351f3bd3ea5..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7adc736ab84b8f1fbceac4f3f1c43bbe7f2086be..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 966fe7eb62c9633e458d4f6726b219ba3708c215..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 31b1196c5962e86ad62d7c31a7e5479a784ce6e1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b74c512decc59aa1f43b22d801b491a33edc700d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c9e74972e052a0147c3cb757c4e708ca48bdbda8..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7d148093bb5f69234a5b2103823d4c81e9e1596c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b664165d6f1c8d21f67a0ec7a9b16ace7708cf32..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2885a3c2f79a7867f7dbb27fda54c4c568f9c643..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 80c06a86c69a70ecb66c88377bcf11b175bb67c3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 07f427837166543299a9d6ccd13941b1555dcc24..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f47c73b886169cd2ccf64d88b3c48d7079eb11ae..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 1514eedad2f0fcd654d5162c43fb07f57d1aeb1f..0000000000000000000000000000000000000000
--- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.err
+++ /dev/null
@@ -1,71 +0,0 @@
-/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
- rep.append(sample.split("_")[2])
-/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
- #if spikes, read json file
-Building DAG of jobs...
-Using shell: /usr/bin/bash
-Provided cores: 1 (use --cores to define parallelism)
-Rules claiming more threads will be scaled down.
-Provided resources: mem_mb=9537, mem_mib=7630, disk_mb=10287, disk_mib=9811, threads=1
-Select jobs to execute...
-Execute 1 jobs...
-
-[Wed Sep 11 15:45:39 2024]
-localrule fastqc:
- input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R2_001.fastq.gz
- output: RES_ATAC/00-Fastqc/ATAC_D0_rep3_R1_001_fastqc.done
- log: RES_ATAC/00-Fastqc/logs/ATAC_D0_rep3_R1_001_fastqc_raw.log
- jobid: 0
- reason: Forced execution
- wildcards: SAMPLE=ATAC_D0_rep3
- resources: mem_mb=9537, mem_mib=7630, disk_mb=10287, disk_mib=9811, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit
-
-
- fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D0_rep3_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D0_rep3_R1_001_fastqc_raw.log
-
-Activating singularity image epeak.sif
-Started analysis of ATAC_D0_rep3_R1_001.fastq.gz
-Approx 5% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 10% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 15% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 20% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 25% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 30% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 35% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 40% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 45% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 50% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 55% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 60% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 65% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 70% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 75% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 80% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 85% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 90% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Approx 95% complete for ATAC_D0_rep3_R1_001.fastq.gz
-Started analysis of ATAC_D0_rep3_R2_001.fastq.gz
-Approx 5% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 10% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 15% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 20% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 25% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 30% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 35% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 40% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 45% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 50% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 55% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 60% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 65% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 70% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 75% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 80% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 85% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 90% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Approx 95% complete for ATAC_D0_rep3_R2_001.fastq.gz
-Touching output file RES_ATAC/00-Fastqc/ATAC_D0_rep3_R1_001_fastqc.done.
-[Wed Sep 11 15:53:26 2024]
-Finished job 0.
-1 of 1 steps (100%) done
-Storing output in storage.
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.out
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d468be2ec2e3ac6cc7de9cff09ab9dc05e6c131f..0000000000000000000000000000000000000000
--- a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.err
+++ /dev/null
@@ -1,71 +0,0 @@
-/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
- rep.append(sample.split("_")[2])
-/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
- #if spikes, read json file
-Building DAG of jobs...
-Using shell: /usr/bin/bash
-Provided cores: 1 (use --cores to define parallelism)
-Rules claiming more threads will be scaled down.
-Provided resources: mem_mb=9537, mem_mib=5353, disk_mb=5613, disk_mib=5353, threads=1
-Select jobs to execute...
-Execute 1 jobs...
-
-[Wed Sep 11 15:45:41 2024]
-localrule fastqc:
- input: /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R1_001.fastq.gz, /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R2_001.fastq.gz
- output: RES_ATAC/00-Fastqc/ATAC_D6F_rep1_R1_001_fastqc.done
- log: RES_ATAC/00-Fastqc/logs/ATAC_D6F_rep1_R1_001_fastqc_raw.log
- jobid: 0
- reason: Forced execution
- wildcards: SAMPLE=ATAC_D6F_rep1
- resources: mem_mb=9537, mem_mib=5353, disk_mb=5613, disk_mib=5353, tmpdir=/pasteur/appa/scratch/rlegendr, mem=10G, threads=1, slurm_partition=hubbioit, slurm_account=hubbioit, slurm_qos=hubbioit
-
-
- fastqc -t 1 --outdir RES_ATAC/00-Fastqc -f fastq /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R1_001.fastq.gz /pasteur/zeus/projets/p01/BioIT/Rachelbis/data_ATAC/ATAC_D6F_rep1_R2_001.fastq.gz > RES_ATAC/00-Fastqc/logs/ATAC_D6F_rep1_R1_001_fastqc_raw.log
-
-Activating singularity image epeak.sif
-Started analysis of ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 5% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 10% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 15% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 20% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 25% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 30% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 35% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 40% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 45% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 50% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 55% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 60% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 65% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 70% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 75% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 80% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 85% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 90% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Approx 95% complete for ATAC_D6F_rep1_R1_001.fastq.gz
-Started analysis of ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 5% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 10% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 15% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 20% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 25% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 30% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 35% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 40% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 45% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 50% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 55% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 60% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 65% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 70% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 75% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 80% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 85% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 90% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Approx 95% complete for ATAC_D6F_rep1_R2_001.fastq.gz
-Touching output file RES_ATAC/00-Fastqc/ATAC_D6F_rep1_R1_001_fastqc.done.
-[Wed Sep 11 15:50:11 2024]
-Finished job 0.
-1 of 1 steps (100%) done
-Storing output in storage.
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.out b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.out
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 440dc14b10f815f69e188f76ac0d380d0bc857c5..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 cd702210985a69f0b011d10f6c9ee1c2d847c077..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 cce2e7e03f34c7fc2b688174c4098340305b1c81..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 59447b30523dfe616c68372dcc4974f38c76e74e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 97e58f38f51350a6eca6f87a724da9b68c59887d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 da8544f73a9e4e0f3a3ffeca8a5583ab45224262..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e77392024caa0fb24dfcc2ad69744bd44890c71d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f1df293db551d7751da179339c05b3f6e39680c1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 28bf78d2024d804dd62cd752e36f295484bfbc80..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d3c3515fd6eb80f25f7b3dc2be3e255277e07dda..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c30716d3eaae6789170f59de9126ec1371658c5e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a91cb77e8ccb0326f913ce30c416e84b862902e2..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 1e831a7237f6080cb61557b8dd5e73e837acd1c1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 fefffd8f71d473a1292b144496349692a5865c69..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d735d03e7967dacea33e72cf87d6674a47ec0141..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 83e76208f47871dd19a76620e72bc707c90ba655..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b76524e58601fc0239813a44bd1386b055879e47..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 773fb2051e2e667fa2481e17fc4c8ab0a70246c1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0e458e08e3b47a94aee5294186eaca583c1ab31c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 db186b0672e4caccdad2602ebc495d380f2f0bed..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f7a5b30d2aca2454d3d15f23f94ff3d11893350e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a91aee65fc530acc28ae5b4dd9035a20969a2d57..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e06aeb2f130db2e549e66fa0688c669c07cfa702..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ed5e4a69dfc2da4fcb3f0e29bd9b971f9fdabebb..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 64a1bae22f382ea613e1d436ae9982357c68dabe..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 8df566d88e68723b94a38115982f252a3219c58f..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ca8d9cedd8907ec532666600212c4a454e833b90..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 364de0d1f57100179adfbb727ea860cc0b237aef..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 bbc80091b1f167a17056a5acfe2791b13c5b15ee..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 8cbcd8e8360ad8dd65c1863ddb3e7f0ee2cfb168..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3d558164f5373847d6c302d7f146cc75e9dcf2fe..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e25a4899d8dbad3e9e60c09c7f87e4728cb54ff2..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 dd81abb2025fa2ad17414fe42c87fc228e8ae9ce..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 74e8b97da9f327641311fcf480d2a56a0c46eda0..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9113df2ca34cf4596067aa469b19759ae9a6935e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 be16ce32913987ba8cd15022dbec4a7eff7388cf..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9a780065bbd7c0b12da2d737f7b4d430c58a2efe..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 fa8861b876aaaa4da22a9176b0edc0665251fc37..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f7dc4d7a5f98ba88da6d462db67ef1c0dd35ff97..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9abcb5cc5c0dcfc09008e1a92d967f2b46a975f2..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 bc3c70fbc37451e84a5a1f1a6cdebfbaa6f2da24..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 482d4768de60ee803ce2408242d4a7080712a247..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7517e545bb04d44b4307b63006c842e062cb4cab..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 86a3ab3877a1d411a74a8fc534d9c9cad54c7808..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7532d34068d9930263e8a520dbeb40b8d20252d7..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9ccb36f4bf725b12e6a3c85cc621393083dd6320..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 bdd8e77bddb5eb3f4df0ee2f3eecbd565ca7602d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 16853132a7817e31b7de1dcc401ad8d88449e813..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d4f3c9b1a06f33c1c9624a319f6f0ab1c272806a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a6d2c01f574bf0a1d731ec0bfd67bca6e96aff19..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 09d928ec6f46ce2ef0a6c13f95ea9b81e56b4046..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a0fce253ebd721b47bf52c1fa5ebdd3712f00b98..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 4f49d7fdc7593a5741889d7af3b7d704e2611efa..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e8dc4dd4add92ed4feadda5b0de648e2acb828fd..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a67ea7d7f9f5c0fa99f7e985fce57fffd69a2434..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2ee80e2a62ea36f40e3c838314bfc45b5e92ee41..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c8c73a3a26b7e0fbd78077b51d0e08a9b12dcd65..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 195eeaf15352550b1069ac472553dabe45fb4800..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f6850a62ec438cc905b68f0d783d0e22c6883d53..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0506951feb09634df8875c83c6f08214c61e0db8..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c3b6fa6849eddc97bfa1b577a8b4135d0dd7eb5f..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3d6188e890aa7da50cba9b39c824f7bc6f1a0a13..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7c5856a475e3d732a5852b38b7355a997a724dbd..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2e863419b0779a28ab3501c28d9a1c48093297b5..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 34074f4da2a129531ba1aac917b41faf353d5e20..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d0bb8b38ba4273b4db18750b50a80b46115e8f78..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 28770ea6aaa1774ad2af9067771c0b7fa24771f0..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e628c8192e2e7ef000e596dbc361c49c89105d8a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 af39fad7d5bd42b4f83157e7e38f96d0631640e5..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 bdabfc3f2acad293be03072dcb3e55d4c0dbdc63..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 16c96d83a1c6331f7b3c103b471e428196977cb3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e9221b8d5e021e8cc252a48324b0ac60ccf21597..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b56ddc20dc40e99f3729d8fbe20d2362285d7004..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 12306c3ec5c52ddc6c8f065abd5a48ee74aa3ec9..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 432e1649d186e4843bad7111254006e3671dfc8a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 41cec468bab3eca63789fffe97ac4c937cb0f8c1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 facfb821057fbb53ea2b7daee53e2852b3406760..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 769f2a18d949a9e8cf03ddd7f1996480285a0dbe..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 1d62d31aa5ef553c02e5ef585905cc4bfc32156c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3c2bd189305f58516f467e570d834dfa24fcfd8a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f33ac7e95859a8ff98f269dc4050651189be8d84..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 cb433b73c04c57b5877ddd71e9b3d12f8f2f1a46..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6a60f0b502e1619bd4fad62e6a4a921f7d1c1966..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d132c8c5e39430a6c918b95f77c152720b5f3e7e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6f11b4ba64d4579f3f122d6d65542c98bdeeb114..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3c5fedc7622d22e622700a5d329562698284ee89..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 af5fc2c44f7a3f6dd8bd40cb3d3dd843a76c56a2..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 232691e5b7e55c33696f70c155b10ac3b3a7d89b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ea9d4422c458cd64c3e9f5b19fa052309ce16147..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5c867f26850b5e2d0385be639bda53ad020aa357..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 89922c839160ee3107d8684298c1b4c95d8d8dba..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 4383bd40e320a97f860a6d0df62e0a1708b2697b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f2bcabcd915d0e0393b456111b331041c3b15480..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2b15b01e534beb5594db0b7368cc3aa4df67dd64..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b13d466b01b48c5b241c934cd13a3ae78b7781e9..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 01c8c53f8e8d97079b5e3baed39bc890b2bc3cbd..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 52c0d4b822fe8b154b13ae132df31ad931fdd369..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3e9bb5060b4514696df40791029deed17dd2d0ef..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 c36ab541eaeebb2953665dfb2652ee3eae6c3d65..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a1514872126b5a05d3e05199c6987d46da64b77d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3301242ec4a44179253cbfc29ccfdba72d03c8ee..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 bada02cb1ee7a41379dfdc4e234c6e71bf70a7ac..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9bcf9dfef959f751c57486d65463a498848ef225..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 293dbd5656136dc3d5c4a9c9044707fc150872a7..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3f7903db4b061e6854ea4a3f20daf06ead0b17c7..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 429123afdd2a8791d20c92956d354314b042e12a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e508280804834e0c2a96f0923ce6b670c6d25416..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5729ce9dae15aba014464d2cbb48a961d81d690d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0e2f100b0f75ade8b5275669ef2ddef96fa7a8f2..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 64ee511775c4bbadc0262c6e20c3031017de77fe..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 1700a92eaece1128497beed12370119e3467d3ec..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2d03ac7f2935cb97dbf603a8aba0096dd180cbcb..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 4443406ffbe93b8d3cf9e9fbf33c3a89f5d93d30..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 08a6251a03b767aa8acda840c668ff9f8d0dfb37..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 17fe60191387bc5c47be1b8dc87fa9d1312c9878..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 bb8561e495d9c3a1a012ac1f3836f59666e10bc8..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 601052255d95929222df03da45e95e12098fbb27..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 26310c447b6bc30a8cbe07a29a9af04582819c4e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6ff9ef280a2f664c51a548b7df49c0fd1dd1fa44..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 80578a13f85d11cf8c3ac0e29c45039e1aabdfb5..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3facf5e963b4342cbfa2244d6832ce46a8f3f39c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2b375e01fa0d3b7a3f3a482e51ec67ee345c94d2..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0a99a961a48397eba82d05a366823c0e8afad534..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 cfe548232c4aa2593f64798720a641ac5fe90a2a..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 e8811b7198789863933238b8eeffffc15fc1d941..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6b30bfd70b2b5cc26a20b69bfbbf0ff6bae85994..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 7657e9d3cce6f6cfd19d30fda89f3ed5d4ca63e4..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 07cae2e4f692ef5fc5dca89d460c5c6bf9948182..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 6b058e3d300f745c7c95848014eb101dcc6babb3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 358bbbd3d8da6acbaa1fa8c924ea409ba973349a..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 aa0d6591af237e8da73a1a3a2512273906e13202..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6851cc4d5eabe3b8f4b15169d80033fb473d33ec..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 538390fad9b92c01fcbf2dcab387c5f448d62fed..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 fddaf8758351aab5bd61ebb7573d4f4d32de6af7..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 b981b989514db18f11f90a01e4bcd2797cf25196..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 bd87e4cacf53ddc88e9d6dd573b1372292cd6f8e..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 c43beb989b044d7199310bc610165e9092e8c537..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b887f1b20b2036b5801a0876b6e892ac84e68815..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 eb37e20ca438efc3cf4a54fb00990227b1414395..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9bc989b76d2dc5ea69caef250b8e8e09ef772ce0..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 d8a380e6060c8c966ae4a6d41666aa60d0f11d55..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e59e46fba0b1324940d2f01f72abf6b0517fc4eb..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 7879798a784734f80c6d7efcd050b6d0fd1b33e0..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 74ac7b2b1fd6dfb7942b6dec9e9de679513271e8..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 12ce8aa4c8bb2c4e959fc1d102abbbf044d9af1b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6d614655ab7a2a066c17ca18ed539703ac268cf8..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 3b2315ed5ff4d7d4bccdf7dfa5029a5ad34b3e1f..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 82d227fab9d0257ef3c75aed98e9e997c9b2c61c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 709fd4bdce1330cd00d251c356c8d6e9d38ed8c1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 4d7a078711b3c53428564af300ce176e6fcced0f..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6fafbfe4b3ae81ad774728524c065eff05339947..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 33021fcb3483b9babd4004624fa0cd93096b9fae..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b851bee5eea9d537c50954152b3a97009572631b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 17805f1085454ae041459a8da005b3c17b3aa74a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 19bb7b2a0a6be35fc6ac6352f69f10e29f7d13c1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a8ad5e9b72dc6ca363e90ac95fa7bbcf8dedda13..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 672745fb3d032d8b64bcb5042e55985ff885869c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 781587859604002bd2df0144787fe021b1e9c213..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2dc1e97bc9632f18f756ba44e9c911e73e9780b4..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f583d61efa529480f7f799beb07b799d1f43f6d2..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 dda107f477fab3c638c03528a072733a94206d9a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/logs/slurm/multiqc/multiqc_unique.err b/logs/slurm/multiqc/multiqc_unique.err
deleted file mode 100644
index bcd14d14d893bdedebfe49d707a76681885f62de..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 864f314327d8277eb6b80b4621a25f2c2886f5b6..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2af1f1ae39cc5eb97678b3e63c8d4b5b5e10fbe2..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0cca8d63980bf72f04cd59b3d27c83e7ae8daf06..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5bd0703ec2f129ecc93a6c02b72fb9a9dcd074b7..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 128af95031dca4f2cf22eae6d881c8f264ae2629..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 bf0171c9c0c52019ba31791a96b6897a136dfc1c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 49b8842da2450ada37b4777a8f398cdef8eb3e0c..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9702dee165580bd7346559f9b4ebfdabbec455a4..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 789a10477555962de7b3e4f5471ec42fcb4e3165..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2ed008e9a96acb85ef34fb248910df784c0c18f3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 386e48b5bf5b92d1e6acc2e715552aefb375fcfe..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b8a365120c7cef63dd03d8110e0bfc9f7693ee7e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 8f4caca664d538540dd681b0531cc0b40a9ed34e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e7890e7d1c7c17b1824967a0ebd56f1f32f6c6c9..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 48c2ba3cdf1cff034ac6dfc6e9168a675504d048..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 583902a0120531295619deb77e048ba1e7c120d1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e3cfb09392209f0eab4a2f09e8bbacb7093b7982..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 be03f8bef69826e73f0011aeb19b749bd2530c68..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 8698ff1e3f42127da5cc008a032042d0890a9ae5..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b438c61a6f9b65edcb765bc6e32e91536c4dcf9b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7f2b5f9f2d8074dd8b8831e1a13da12f0d2f113f..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5bd8bb67643a3f589dcce42a00f29a0aa401b70a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b47651ac687446003c42315ef4d190b9bfeed134..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b761fee6cac3f95ae70006d4e09453ca77296239..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 4d65f708bf51076a5a5d5a4e3b11115b00f0956b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 264b02ecf4acb4b7e6c70381c94082498f71c72e..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 228b446f2b7866cc2042c0e880b9b17c83c7aca1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 13ba74094c2a8db0305c6c5d1bef21a5831cf458..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0b1b7e19cc5ceb17dbe36162b5a04a80c179ae68..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a773013611d8e2dc136aa3664f255b58645f1fa1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2a8c852f69010662981dea844b6ee62bece592a8..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3928254d5e87998fd3dccd95896d267804ad51da..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 8f1959bc0f93d8f495c2ad067722ac7932a766d5..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 359eabae97e6260e93bd3caa467c93be6e596f05..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 a445d77e39186c98b2b9b047e7b116bf1ce7d1fa..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 300c777c451d4719df5a44a048d7fba732e9f100..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 13bf7e0d6ed7613a06a35b672778ebd90f455773..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e81959fd2795c3c45f0a6a3efc8b5acc474e1a83..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 d6eb724db29eae90c465605047c01df98fe18291..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 845b38cf9f57986df36dfebf6ad68766a01253e8..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 7bab108c6ec841495bf6a7a0695f3b852546116f..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e9e57ba1c7f3300c6e619fe6c74b09bcc19c16b2..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 194a6d40d771aa12fc4ad06d0341612a0da5ae85..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e1017bd6d0c1b52b2bee56b6e8514d2f2154c007..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 3469839405233d751c320ed795dc4947a0b01e57..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b3049ec7df32047a48fa12f41443074db1b7d8ee..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 0c7785841c462713cdd81d9d42ba4d53a38ba491..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0efe08d6ffd018f30c7949040e558f1fe0dc47e6..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 31dc03328515bcd192cb221ebd7c3d62b817b265..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 2da87236b390a01af0f51e1ead5ed6861f04eced..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 3cf607fa7969e73f9c29e560a853da05c1efb421..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9a7d168da5cc75471fe1afd162c25d7b53609e28..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 5fae6a4080cc59995aaaede93b81984aca066270..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b2a681d1f721945507dc0c1866d257f00ca50aac..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 068746d1babb0df0f1a2946aec7f5300d2f3bd71..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9f313e7a70ab0764d0b871d83c73eac6c56cdd77..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 45aff0d78e28401d95a90da6c4d3e008f09ab594..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 973218b87cf248ba97ca6777bbb105d877449070..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 e3dce91c8f62a0418c86dfc6fdff027359dabb46..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 8e4d845f1c9d1b55c6cf5a1d8eaad13708cd17df..0000000000000000000000000000000000000000
--- 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 0cfbf08886fca9a91cb753ec8734c84fcbe52c9f..0000000000000000000000000000000000000000
--- 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 cc7effbe1e58abdd1d210ff4532ed94705cbd8bf..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 b01318e8312f5d9f4266466c710b6cc057b1e612..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 9f4496a7fc18ae4f4760897c95e9a8903ec2c3bd..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d837738ff5f955ba11fef7b3bb1a60c65fd915b7..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 f3fa866fdf97f0c61dc584208da7180b88ca2b24..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 ac5d5321a8d6a7fa62fc442e02eae3ee89c60d52..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3db34c69b2fcb01b9cd10e19043a5f490621d28a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 3eb9143707c363d13c4a43fb5e5e18cd828d9473..0000000000000000000000000000000000000000
--- 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 9a099f9e71b88cb61581276fa58f6ae43c860705..0000000000000000000000000000000000000000
--- 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 1f62e641d5feccc6872021959dd89da29d3bc147..0000000000000000000000000000000000000000
--- 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 9a099f9e71b88cb61581276fa58f6ae43c860705..0000000000000000000000000000000000000000
--- 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 81b491ab78b5b49afc50651d7f6ffd7d759e642f..0000000000000000000000000000000000000000
--- 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 9a099f9e71b88cb61581276fa58f6ae43c860705..0000000000000000000000000000000000000000
--- 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 cbbfd12a27496f83d94cecf60adc2034df07928d..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e9b668a7187938010e4dbb1d89df67db4e6e81da..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 26c59de27f19282f4821345f17b0524ed74754b1..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d744b283e9d36922051572d2d9c7e50b34dc44d3..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 901a6e0517baf3e4f98a1250abcef48b3c890642..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0c38c3d7f61eb00311079cc447fe725e351896c6..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 547cf865c6edea7850affa58517d1ecfc501ea22..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e75d0f48eb27591baf3f8f2335f19c117159e550..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 6f4f6d4571a6e56022e8aa059ce5b80c6e91508f..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0ad8e7abf6a8a74626a8d188fc4aa0159015187a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 39691c7e95455ba1eba09047f1dd8ffbba3a4ee0..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 0cfefe83335e940b2a868b763e73ee9f823722b0..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 4094277d3fb3ee1e0d7257ed477bf4c6b676c69b..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 5d9b4cf086275e7209adc8ef9372ed0ca2317fac..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 7cb00d5d9a07084610b09b25e6ed342fd939fbd8..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 06cd73078c7f39a2e59cafe5c5888f8a72ade18a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 d41e811b1e292c5442b22e1097fc4a4924feba8a..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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 e5d5c5c0c21b9887e9655d8948fc3b6500bf4568..0000000000000000000000000000000000000000
--- 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 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/singularity/.gitkeep b/singularity/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/singularity/epeak.def b/singularity/epeak.def
deleted file mode 100644
index ff24f8e5fe6243ffeeb766fdd8b2839aaad60367..0000000000000000000000000000000000000000
--- 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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