diff --git a/README.md b/README.md
index 9ce71e5035d44d22465ce298dfc682dfaf168aca..424070d4599bae5874e2f812f29870cd34733f40 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@
-[](https://snakemake.readthedocs.io/en/stable/) [](https://www.python.org/downloads/release/python-360/) [](https://docs.sylabs.io/guides/3.0/user-guide/quick_start.html)
+[](https://snakemake.readthedocs.io/en/stable/) [](https://www.python.org/downloads/release/python-360/) [](https://docs.sylabs.io/guides/3.0/user-guide/quick_start.html)
## Table of content
@@ -20,30 +20,32 @@ ePeak is a snakemake-based workflow for the analysis of ChIP-seq/CUT&RUN/CUT&Tag
# How to install ePeak ?
-## Installation with singularity
+## Installation with apptainer
Pre-required tools:
- python >= 3.8
-- snakemake >=4.8.0
+- snakemake >=7.18.2
- pandas >= 2.0.0
- pysam
-- singularity >= 3.8
+- apptainer >= 1.2.5
A tutorial to create a conda environment with all dependencies is available here : [env.sh](https://gitlab.pasteur.fr/hub/ePeak/-/blob/master/env.sh)
-Download the singularity container:
+Download the apptainer container:
-` singularity pull --arch amd64 --name epeak.img library://rlegendre/epeak/epeak:1.0`
+`apptainer pull --arch amd64 --name epeak.img library://rlegendre/epeak/epeak:2.0`
+
+> Note: Please configure apptainer before to pull the image.
## Manual installation
List of tools to install:
- python >= 3.8
-- snakemake >=4.8.0
+- snakemake >=7.18.2
- pandas
- pysam
-- singularity
+- apptainer >= 1.2.5
- cutadapt >= 3.2
- fastqc == 0.11.9
- samtools >= 1.10
@@ -75,11 +77,11 @@ module load pysam
`git clone https://gitlab.pasteur.fr/hub/ePeak.git`
-* Download singularity container:
+* Download apptainer container:
```
cd ePeak
-singularity pull --arch amd64 --name epeak.img library://rlegendre/epeak/epeak:1.0
+apptainer pull --arch amd64 --name epeak.sif library://rlegendre/epeak/epeak:2.0
```
Then, you can configure the workflow.
@@ -96,7 +98,7 @@ Then, you can configure the workflow.
In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, its DOI (see [above](https://gitlab.pasteur.fr/hub/ePeak#how-to-cite-ePeak-))
-If you are using Singularity, you need to copy the Singularity image in the cloned ePeak directory.
+If you're using apptainer, you need to copy the apptainer image into the cloned ePeak directory (snakemake version 7). For snakemake version 8, specify the container path via profile/config.yaml.
* Step 2: Configure workflow
@@ -110,23 +112,11 @@ In addition, you can customize the MultiQC report by configuring this file: [mul
Test your configuration by performing a dry-run via:
-`snakemake --use-singularity -n --cores 1`
+`snakemake -n --cores 1`
Execute the workflow locally using $N cores via:
-`snakemake --use-singularity --singularity-args "-B '/home/login/'" --cores $N`
-
-Run it in a cluster environment via this standard command line:
-
-`snakemake --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
-
-Or specifically on Slurm cluster:
-
-`sbatch snakemake --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores $SLURM_JOB_CPUS_PER_NODE`
-
-or on SGE cluster:
-
-`snakemake --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "qsub -cwd -V -b y -l h_vmem={cluster.ram} -pe [PE] {threads}" -j 200 --nolock --cores 1`
+`snakemake --use-apptainer --apptainer-args "-B '/home/login/'" --cores $N`
Visualize how the rules are connected via:
@@ -169,6 +159,23 @@ When your `profile/config.yaml` is ready, and all parameters sets as you want yo
### Snakemake version 7
+- without profiles
+
+Run it in a cluster environment via this standard command line:
+
+`snakemake --use-apptainer --apptainer-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
+
+Or specifically on Slurm cluster:
+
+`sbatch snakemake --use-apptainer --apptainer-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores $SLURM_JOB_CPUS_PER_NODE`
+
+or on SGE cluster:
+
+`snakemake --use-apptainer --apptainer-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "qsub -cwd -V -b y -l h_vmem={cluster.ram} -pe [PE] {threads}" -j 200 --nolock --cores 1`
+
+
+- with profiles
+
A similar way to use snakemake is possible with the version 7, and for that you just have to follow the same recipe as before but the plugins are not the same.
An already existing and functional `config.yaml` is present in the `profile_v7/`.
Run the pipeline in snakelake v7 is possible with:
@@ -266,6 +273,9 @@ tmpdir: "/tmp/"
The design chunk aims to check that the FASTQ files name match the design file information. The `marks`, `conditions` and `replicates` parameters must respectively match the *MARK*, *COND* and *REP* parameters of the FASTQ files name and the design file.
For spike-in data, set `spike` on "True" and provide the spike-in genome FASTA file path through the `spike_genome_file` parameter.
+> The mate pairs regular expression is utilized by the pipeline to to automatically detect whether the data is single or paired-end. The use of [] and the inclusion of two possible numbers are mandatory.
+
+
```
design:
design_file: /path/to/directory/analysis/config/design.txt
@@ -303,7 +313,7 @@ bowtie2_mapping:
If you choose to execute the Peak annotation rule, you have the possibility to do it in 2 ways : standard and non standard. If you choose to do it in a non-standard way you must specify in the annotation_config file the relative path for any reference_file parameters in the theme blocks.
-Moreover some files can be used for annotation (see Annotk user guide), and if a txt file can be used be carefull that it is not a gff to txt file, since the header must have at least 'Gene ID' in it.
+Moreover some files can be used for annotation (see [Annotk user guide](https://gitlab.pasteur.fr/hub/ePeak/-/blob/master/test/annotation/Annotation/Annotation-readme.pdf)), and if a txt file can be used be carefull that it is not a gff to txt file, since the header must have at least 'Gene ID' in it.
### How to fill the multiqc config
@@ -364,6 +374,9 @@ intersectionApproach:
> If none or very few peaks pass the IDR, this means that there is to much variability between your replicates aka they are probably not good replicates. If you want to proceed anyway with the analysis, you can use the intersection approach (less stringent) instead of the IDR by setting `intersectionApproach` to 'yes'.
+> If you have more than 2 replicates, you can use Chipr instead of IDR, as the results are quite similar.
+
+
### Default broad mode with intersection approach
In broad mode, perform a stringent peak calling (cutoff of 0.01) and use Intersection Approach. Overlapping parameter of IA on broad peaks is set at 0.8.
@@ -464,7 +477,41 @@ intersectionApproach:
To run the pipeline, the correct Snakefile (Snakefile_noCTL) should be used:
-`snakemake -s Snakefile_noCTL --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
+`snakemake -s Snakefile_noCTL.smk --use-apptainer --apptainer-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
+
+
+or using Snakemake Profile:
+
+`snakemake -s Snakefile_noCTL.smk --workflow-profile profile/`
+
+
+### ATAC-seq mode
+
+To analyze ATAC-seq data, ePeak now offers an update that takes into account the specific features of accessibility data.
+
+First, fill in the design file in the same way as for the previous mode without INPUT:
+
+
+```
+IP_NAME NB_IP
+ATAC_D0 3
+ATAC_D2 3
+ATAC_D6 3
+```
+
+Then fill the [config_atac.yaml](https://gitlab.pasteur.fr/hub/ePeak/-/blob/master/config/config_atac.yaml) with dedicated peak callers (MACS3, Genrich, LanceOtron).
+
+All the other features of the standard epeak pipeline are still available (preprocessing including specific quality control, peak annotation and differential analysis, etc.).
+
+
+To run the pipeline, the correct Snakefile (Snakefile_atac.smk) should be used:
+
+
+`snakemake -s Snakefile_atac.smk --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
+
+or using Snakemake Profile:
+
+`snakemake -s Snakefile_atac.smk --workflow-profile profile/`
@@ -516,14 +563,26 @@ done
Run it in a cluster environment via this standard command line:
-`snakemake --configfile test/config/config.yaml --use-singularity --singularity-args "-B '$HOME'" --cluster-config test/config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
+`snakemake --configfile test/config/config.yaml --use-apptainer --apptainer-args "-B '$HOME'" --cluster-config test/config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1`
> by default, ePeak always use the multiqc_config.yaml in the config directory
# Q&A
-**What's a IP?**
+**I couldn't download the apptainer image, I got this error: remote has no library client**.
+- Before downloading the apptainer image, make sure you configure your client correctly with this command: `apptainer remote add --no-login SylabsCloud cloud.sylabs.io`
+
+**I'm getting an error using Profile (about cluster-generic), I don't understand**.
+- You need to install specific packages to launch a snakemake pipeline with profiles. Make sure you have installed `snakemake-executor-plugin-slurm` and `snakemake-executor-plugin-cluster-generic` via pip.
+
+**I can run the pipeline with snakemake v < 8. * . * ?**
+- Yes, you can run snakemake with a version of snakemake lower than v.8, to do this you need to use the profile inside the profile_v7 directory, in which you'll find a config.yaml file that you can customize with the specifics of your cluster. The command line to run should be `--profile profile_v7/` .
+
+**I have single-end reads and I don't know how to fill the mate pair format ?**
+- The pipeline is designed to automatically detect whether or not data is sequenced with a regex. When you define “\_R[12]”, the pipeline will search for files with tags \_R1 and \_R2, or if you specify “\_[12]\_001”, the pipeline will search for files with tags \_1\_001 or \_2\_001. If only one tag is found, ePeak knows that you have single-ended data.
+
+**What's a IP?**
- IP stand for ImmunoPrecipitation. The IP samples contains the DNA that bind the protein of interest (i.e. H3K4me1, CTCF, TFIIA). These samples has been cross-linked, sonicated and immuno-precipitated.
**What's an INPUT?**
@@ -578,26 +637,35 @@ Run it in a cluster environment via this standard command line:
**When should I use PhantompeakCalling's fragment size estimation instead of MACS2's one?**
- If MACS2 cannot compute the fragment size estimation (or if you want), set `no_model` to yes, and the fragment length use for MACS2 will be the one computed by PhantompeakQualTools for each sample.
-**What if I don't know if my chromatim factor in narrow or broad?**
-- The output directories names of peak Calling, peak reproducibility and differential analysis steps includes the peak calling mode name, the peak reproducibility method name and the normalisation and variance estimation method name. This allows ePeak to test multiple combinations of peak calling, peak reproducibility and differential analysis parameters without erasing any output.
-- For example, if you have run the pipeline in narrow mode, and you want broad mode, you just need to modify the corresponding parameter in the configuration YAML file. The pipeline will then restart at the peak calling step and all the output will be stored in "06-PeakCalling/{}" directories.
-- In case of unknown chromatin factor, we advice to run ePeak in narrow mode with IDR and IA, and afterward in broad mode. Results from narrow peak calling will be stored in "06-PeakCalling/Narrow" directory, and in "06-PeakCalling/Broad" for broad peak calling.
-
-**Can I run the pipeline with snakemake v < 8. * . * ?**
-- Yes you can run snakemake with a version of snakemake below to v.8, for that you have to use the profile inside the directory profile_v7. Inside you will find a config.yaml file that you can custom with your cluster specificities. The command line to execute has to be with `--profile profile_v7/` .
+**What if I don't know whether my chromatic factor is narrow or broad?**
+- The output directory names of the peak calling, peak reproducibility and differential analysis steps include the name of the peak calling mode, the name of the peak reproducibility method and the name of the normalization and variance estimation method. This allows ePeak to test several combinations of peak calling, peak reproducibility and differential analysis parameters without deleting any output.
+- For example, if you've run the pipeline in narrow mode and want to run it in broad mode, simply change the corresponding parameter in the YAML configuration file. The pipeline will then restart at the peak calling stage and all results will be stored in the “06-PeakCalling/{}” directories.
+- In the case of an unknown chromatin factor, we recommend running ePeak in narrow mode with IDR and IA, then in broad mode. The results of narrow peak calling will be stored in the “06-PeakCalling/Narrow” directory, and in “06-PeakCalling/Broad” for broad peak calling.
**Can I use Hmmratac?**
-- Hmmratac is present in the pipeline but for the moment some parameters needed for the rest of the analysis are missing to the output files that it return. You can still run it but the output from Hmmratac will not pass throught the rest of the pipeline and, we can not tell anything confidently on peaks found by this peak caller.
-- If thoses parameters can be present it can be usefull to run Hmmratac a first time and then adjusting the parameters after.
+- Hmmratac is present in the pipeline, but for the moment some of the parameters needed for the rest of the analysis are missing from the output files it returns. You can still use it, but Hmmratac's output won't pass through the rest of the pipeline and we can't say anything with confidence about the peaks found by this peak caller.
+- If these parameters are present, it may be worth running Hmmratac once and adjusting the parameters afterwards.
+
+
+
+
---
# Authors
-* Rachel Legendre (@rlegendr)
-* Maëlle Daunesse
-* Adrien Pain
-* Hugo Varet
-* Claudia Chica
+* Rachel Legendre (@rlegendr), Research engineer Institut Pasteur
+* Maëlle Daunesse, Research engineer Institut Pasteur
+* Adrien Pain, Research engineer Institut Pasteur
+* Hugo Varet, Research engineer Institut Pasteur
+* Claudia Chica, Research engineer Institut Pasteur
+
+# Contributors
+
+* Luc Jouneau, Research engineer from INRAE
+* Amina Alioua, Sorbonne M2 student
+* Meije Mathé, Rouen University M2 student
+* Victoire Baillet, Research engineer Institut Pasteur
+
# How to cite ePeak ?
diff --git a/Snakefile b/Snakefile
index a4841526f2fc98f8d390253ca7cf98a839a316ba..953e159c3ccf5744db49b20d35650954a45c0d4c 100755
--- a/Snakefile
+++ b/Snakefile
@@ -376,7 +376,6 @@ wildcard_constraints:
#any path separator
CALLER="[^/]+",
IP_IDR="[^/]+",
-
sample = "[A-Za-z-_0-9]+_{0}[0-9]+".format(rep_flag),
IP_REP = "[A-Za-z-_0-9]+_{0}[0-9]+".format(rep_flag),
REP = "{0}[0-9]+".format(rep_flag),
@@ -905,7 +904,7 @@ if config["chipr"]["do"] and config["macs2"]["do"]:
chipr_output_opti = os.path.join(analysis_dir,"08-ReproduciblePeaks/{CALLER}/Chipr/{MARK}_{COND}_DONE_optimal.bed")
chipr_output_all = os.path.join(analysis_dir,"08-ReproduciblePeaks/{CALLER}/Chipr/{MARK}_{COND}_DONE_all.bed")
chipr_output_log = os.path.join(analysis_dir,"08-ReproduciblePeaks/{CALLER}/Chipr/{MARK}_{COND}_DONE_log.txt")
-
+ chipr_options = config["chipr"]["options"]
chipr_tmp = os.path.join(analysis_dir,"08-ReproduciblePeaks/{CALLER}/Chipr/{MARK}_{COND}_tmp")
chipr_log = os.path.join(analysis_dir,"08-ReproduciblePeaks/{CALLER}/Chipr/logs/{MARK}_{COND}_log")
chipr_log_err = os.path.join(analysis_dir,"08-ReproduciblePeaks/{CALLER}/Chipr/logs/{MARK}_{COND}_log_err")
@@ -1048,20 +1047,30 @@ if config["peakAnnotation"]["do"] and (
#----------------------------------
# Run differential analysis
#----------------------------------
+CALL_MOD = []
if len(conds) > 1 and config["differential_analysis"]["do"]:
-
+ if config["macs2"]["do"] and model in ["narrow"] and not config["intersectionApproach"]["do"] and config["compute_idr"]["do"] or config["chipr"]["do"]:
+ CALL_MOD += ["macs2_" + model_dir]
+ if config["seacr"]["do"] :
+ CALL_MOD += ["seacr_" + config["seacr"]["threshold"]]
+ if (config["macs2"]["do"] and config["intersectionApproach"]["do"]) or (config["macs2"]["do"] and config["macs2"]["mode_choice"] in ["broad"]):
+ CALL_MOD += ["macs2_" + model_dir]
+
+ ## fill CALL_MOD according to results....
def getPeakFilesByMark(wildcards):
if wildcards.CALLER in ["seacr_"+config["seacr"]["threshold"], "macs2_broad", "macs2_broad-nomodel" ] or (wildcards.CALLER in ["macs2_narrow","macs2_narrow-nomodel"] and config["intersectionApproach"]["do"]):
- return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/{MARK}_{COND}_IA.bed"),
+ return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{{CALLER}}/{{MARK}}_{COND}_IA.bed"),
CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds)
+ elif config["chipr"]["do"] and config["macs2"]["do"] and not config["compute_idr"]["do"]:
+ return expand(os.path.join(analysis_dir,"08-ReproduciblePeaks/{{CALLER}}/Chipr/{{MARK}}_{COND}_DONE_optimal.bed"),
+ CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds)
else :
return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{{CALLER}}/{{MARK}}_{{COND}}_select.{}Peak".format(model)),
CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds)
-
#----------------------------------
# get union peaks
#----------------------------------
@@ -1151,6 +1160,7 @@ if len(conds) > 1 and config["differential_analysis"]["do"]:
chipflowr_init_output_dir = os.path.join(analysis_dir, "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}".format(method, norm))
chipflowr_init_config_r = os.path.join(analysis_dir, "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/config.R".format(method, norm))
chipflowr_init_genome = ref
+ final_output.extend(expand(chipflowr_init_config_r, CALLER=CALL_MOD, MARK=MARK_OK))
include: os.path.join(RULES, "chipflowr_init.rules")
@@ -1164,15 +1174,17 @@ if len(conds) > 1 and config["differential_analysis"]["do"]:
#----------------------------------
# differential analysis annotation
#----------------------------------
- #LJO 20240226 : Je mets en condition d'entree un fichier de sortie de l'analyse differentielle
- # Si je mets un repertoire, cela ne marche pas
- diffannot_input_dir=chipflowr_report
- diffannot_output_dir = os.path.join(analysis_dir, "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/annotated_results".format(method, norm))
- diffannot_logs = os.path.join(analysis_dir,
- "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/annotated_results/annotation.log".format(method, norm)
- )
- include: os.path.join(RULES, "chipflowr_annotation.rules")
- final_output.extend(expand(diffannot_output_dir, CALLER=CALL_MOD, MARK=MARK_OK))
+ if config["peakAnnotation"]["do"]:
+ #LJO 20240226 : Je mets en condition d'entree un fichier de sortie de l'analyse differentielle
+ # Si je mets un repertoire, cela ne marche pas
+ diffannot_input_dir = chipflowr_report
+ diffannot_output_dir = os.path.join(analysis_dir, "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/annotated_results".format(method, norm))
+ diffannot_logs = os.path.join(analysis_dir,
+ "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/annotated_results/annotation.log".format(method, norm)
+ )
+ diffannot_output_done = os.path.join(analysis_dir,"10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/annotated_results/annotation.done".format(method, norm))
+ include: os.path.join(RULES, "chipflowr_annotation.rules")
+ final_output.extend(expand(diffannot_output_done, CALLER=CALL_MOD, MARK=MARK_OK))
#----------------------------------
# IGV session
diff --git a/Snakefile_atac.smk b/Snakefile_atac.smk
index 2a47c07be432c045ccd79a037525a3390e5745bb..18b72ffc9ddbbcd3bf099a7b5d6a11699c5220d3 100755
--- a/Snakefile_atac.smk
+++ b/Snakefile_atac.smk
@@ -268,10 +268,6 @@ wildcard_constraints:
sample = "[A-Za-z-_0-9]+_{0}[0-9]+".format(rep_flag),
IP_REP = "[A-Za-z-_0-9]+_{0}[0-9]+".format(rep_flag),
REP = "{0}[0-9]+".format(rep_flag),
- SPR = "[A-Za-z-_0-9]+_SPR[0-9]\.[1-4]*",
- PPR = "[A-Za-z-_0-9]+_PPR[0-9]*",
- POOL = "[A-Za-z-_0-9]+_PPRPool",
- INPUT_POOL = "[A-Za-z-_0-9]+_(Pool|{0}1)".format(rep_flag),
MARK = "[A-Za-z-_0-9]+",
COND = "[A-Za-z-_0-9]+"
@@ -688,8 +684,8 @@ if config["chipr"]["do"]:
metrics_chipr_output = os.path.join(analysis_dir, "CHIPR_{CALLER}_{MOD}_{FORM}_metrics.out")
include: os.path.join(RULES, "metrics_chipr.rules")
- for peak_caller in all_peak_caller.keys():
- final_output.extend(expand(metrics_chipr_output,CALLER=peak_caller,MOD=all_peak_caller[peak_caller][0],FORM=all_peak_caller[peak_caller][1]))
+ #for peak_caller in all_peak_caller.keys():
+ # final_output.extend(expand(metrics_chipr_output,CALLER=peak_caller,MOD=all_peak_caller[peak_caller][0],FORM=all_peak_caller[peak_caller][1]))
#----------------------------------
@@ -778,11 +774,15 @@ if len(all_peak_caller.keys()) >= 1:
# To recheck can cause a break if mutliple conds but with different marks are there
# Better gestion of conds ?
+
if len(conds) > 1 and config["differential_analysis"]["do"]:
-
def getPeakFilesByMark(wildcards):
- return expand(os.path.join(analysis_dir,"08-ReproduciblePeaks/{{CALLER}}_{{MOD}}/IA_{FORM}/{MARK}_{COND}_IA.bed"),FORM=FORMAT,MARK=MARK_OK,COND=conds)
+ if len(all_peak_caller.keys()) > 0 and config["intersectionApproach"]["do"]:
+ return expand(os.path.join(analysis_dir,"08-ReproduciblePeaks/{{CALLER}}_{{MOD}}/IA_{FORM}/{MARK}_{COND}_IA.bed"),FORM=mod,MARK=MARK_OK,COND=conds)
+ elif config["chipr"]["do"]:
+ return expand(os.path.join(analysis_dir,"08-ReproduciblePeaks/{{CALLER}}_{{MOD}}/Chipr_{FORM}/{MARK}_{COND}_DONE_optimal.bed"), FORM=mod,MARK=MARK_OK,COND=conds)
+
#----------------------------------
# get union peaks
#----------------------------------
@@ -821,13 +821,15 @@ if len(conds) > 1 and config["differential_analysis"]["do"]:
for peak_caller in all_peak_caller.keys():
final_output.extend(expand(bed_to_gff_output, CALLER=peak_caller,MOD=all_peak_caller[peak_caller][0], MARK=MARK_OK))
- def getBAMFilesByMark(wildcards):
- return expand(os.path.join("%s/{MARK}_{COND}_{REP}_%s_sort%s.bam" % (biasedRegions_dir, ref, biasedRegions)),
- MARK=MARK_OK, COND=conds, REP=rep_noidr)
-
+
#----------------------------------
# feature Count on peaks
#----------------------------------
+
+ def getBAMFilesByMark(wildcards):
+ return expand(os.path.join("%s/{MARK}_{COND}_{REP}_%s_sort%s.bam" % (biasedRegions_dir, ref, biasedRegions)),
+ MARK=MARK_OK, COND=conds, REP=rep_noidr)
+
feature_counts_input = getBAMFilesByMark
feature_counts_output_count = os.path.join(analysis_dir, "09-CountMatrix/{CALLER}_{MOD}/{MARK}_Matrix_Optimal_Peak.mtx")
diff --git a/Snakefile_noCTL.smk b/Snakefile_noCTL.smk
index bc8ddbc07cc4b4bbe4a5adc486e92aea9126b497..756a6b23463f21f223bd4c2521e543798e054117 100755
--- a/Snakefile_noCTL.smk
+++ b/Snakefile_noCTL.smk
@@ -912,19 +912,28 @@ if config["peakAnnotation"]["do"] and (
# Run differential analysis
#----------------------------------
+CALL_MOD = []
+
if len(conds) > 1 and config["differential_analysis"]["do"]:
-
+ if config["macs2"]["do"] and model in ["narrow"] and not config["intersectionApproach"]["do"] and config["compute_idr"]["do"] or config["chipr"]["do"]:
+ CALL_MOD += ["macs2_" + model_dir]
+ if config["seacr"]["do"] :
+ CALL_MOD += ["seacr_" + config["seacr"]["threshold"]]
+ if (config["macs2"]["do"] and config["intersectionApproach"]["do"]) or (config["macs2"]["do"] and config["macs2"]["mode_choice"] in ["broad"]):
+ CALL_MOD += ["macs2_" + model_dir]
+
+ ## fill CALL_MOD according to results....
def getPeakFilesByMark(wildcards):
if wildcards.CALLER in ["seacr_"+config["seacr"]["threshold"], "macs2_broad", "macs2_broad-nomodel" ] or (wildcards.CALLER in ["macs2_narrow","macs2_narrow-nomodel"] and config["intersectionApproach"]["do"]):
- return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/{MARK}_{COND}_IA.bed"),
+ return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{{CALLER}}/{{MARK}}_{COND}_IA.bed"),
CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds)
+ elif config["chipr"]["do"] and config["macs2"]["do"] and not config["compute_idr"]["do"]:
+ return expand(os.path.join(analysis_dir,"08-ReproduciblePeaks/{{CALLER}}/Chipr/{{MARK}}_{COND}_DONE_optimal.bed"),
+ CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds)
else :
return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{{CALLER}}/{{MARK}}_{{COND}}_select.{}Peak".format(model)),
CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds)
-
-
-
#----------------------------------
# get union peaks
#----------------------------------
@@ -1027,15 +1036,16 @@ if len(conds) > 1 and config["differential_analysis"]["do"]:
#----------------------------------
# differential analysis annotation
#----------------------------------
- #LJO 20240226 : Je mets en condition d'entree un fichier de sortie de l'analyse differentielle
- # Si je mets un repertoire, cela ne marche pas
- diffannot_input_dir=chipflowr_report
- diffannot_output_dir = os.path.join(analysis_dir, "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/annotated_results".format(method, norm))
- diffannot_logs = os.path.join(analysis_dir,
- "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/annotated_results/annotation.log".format(method, norm)
- )
- include: os.path.join(RULES, "chipflowr_annotation.rules")
- final_output.extend(expand(diffannot_output_dir, CALLER=CALL_MOD, MARK=MARK_OK))
+ if config["peakAnnotation"]["do"]:
+ #LJO 20240226 : Je mets en condition d'entree un fichier de sortie de l'analyse differentielle
+ # Si je mets un repertoire, cela ne marche pas
+ diffannot_input_dir=chipflowr_report
+ diffannot_output_dir = os.path.join(analysis_dir, "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/annotated_results".format(method, norm))
+ diffannot_logs = os.path.join(analysis_dir,
+ "10-DifferentialAnalysis/{{CALLER}}/{{MARK}}_{}_{}/annotated_results/annotation.log".format(method, norm)
+ )
+ include: os.path.join(RULES, "chipflowr_annotation.rules")
+ final_output.extend(expand(diffannot_output_dir, CALLER=CALL_MOD, MARK=MARK_OK))
#----------------------------------
# IGV session
diff --git a/apptainer/.gitkeep b/apptainer/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/apptainer/epeak_v1.0.def b/apptainer/epeak_v1.0.def
new file mode 100644
index 0000000000000000000000000000000000000000..ff24f8e5fe6243ffeeb766fdd8b2839aaad60367
--- /dev/null
+++ b/apptainer/epeak_v1.0.def
@@ -0,0 +1,131 @@
+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
+
+
+
+
+
+
+
+
+
diff --git a/apptainer/epeak_v2.0.def b/apptainer/epeak_v2.0.def
new file mode 100644
index 0000000000000000000000000000000000000000..cb47835ead5f9f7a3cdf5fc0112bbed6bbd4c887
--- /dev/null
+++ b/apptainer/epeak_v2.0.def
@@ -0,0 +1,149 @@
+BootStrap: docker
+From: ubuntu:22.04
+
+%post
+
+ cd /opt
+
+ export DEBIAN_FRONTEND=noninteractive
+
+ apt update -y
+ apt upgrade -y
+
+ apt -y install locales
+ locale-gen en_US.UTF-8
+ 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
+
+ # install python and common tools
+ apt install -y python3-full python3-dev python3-setuptools
+ apt install -y python3-pip curl unzip wget git gzip tar
+ apt install -y python3-numpy python3-matplotlib python3-scipy python3-pysam cython3
+ apt install -y fastqc bowtie2 picard-tools subread bedtools
+ apt install -y build-essential libcurl4-gnutls-dev libgit2-dev libharfbuzz-dev libfribidi-dev gfortran #for devtools package
+ apt install -y gcc make libbz2-dev zlib1g-dev libncurses5-dev libncursesw5-dev liblzma-dev libfontconfig1-dev
+
+
+ # Créez le script wrapper pour `picard`
+ echo '#!/bin/bash' > /usr/local/bin/picard
+ echo 'PicardCommandLine "$@"' >> /usr/local/bin/picard
+ chmod +x /usr/local/bin/picard
+
+ #install pip tools
+ pip install pysam cutadapt macs2
+ pip install multiqc
+ pip install deeptools
+ pip install bx-python
+ pip install MACS3
+ pip install lanceotron
+ pip install ChIP-R
+
+ #install recent versio of samtools
+
+ wget https://github.com/samtools/samtools/releases/download/1.20/samtools-1.20.tar.bz2
+ tar xvf samtools-1.20.tar.bz2
+ cd samtools-1.20
+ ./configure
+ make
+ make install
+
+
+ #install IDR
+ wget https://github.com/nboley/idr/archive/2.0.3.zip
+ unzip 2.0.3.zip
+ cd idr-2.0.3/
+ perl -i -pe 's/'numpy.int/numpy.int_/g'' idr/idr.py #https://github.com/nboley/idr/issues/64
+ python3 setup.py install
+
+ #install R and dependancies
+ 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
+
+
+ cd /opt
+ #ln -s /bin/gzip /usr/bin/gzip
+ #ln -s /bin/tar /usr/bin/tar
+ export TAR="/bin/tar"
+
+
+ apt install -y pandoc
+ apt update -y
+ apt install -y pandoc-citeproc
+
+ apt install -y build-essential libgit2-dev libharfbuzz-dev libfribidi-dev gfortran libreadline-dev #for devtools package
+ apt install -y software-properties-common
+ apt install -y libx11-dev libxext-dev libxt-dev
+
+ apt update -y
+ apt upgrade -y
+
+ #apt-cache showpkg r-base
+ apt install -y r-base
+
+
+ #install SPP
+ 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
+
+
+ # install ChipFlowR
+ echo 'install.packages("remotes", repos="http://cran.us.r-project.org", dependencies=TRUE)' > chipflowr.txt
+ echo 'library(remotes)' >> 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 'remotes::install_gitlab(repo="hub/chipflowr", host="gitlab.pasteur.fr", build_vignettes=TRUE)' >> chipflowr.txt
+ Rscript chipflowr.txt
+
+
+
+%environment
+ ## export all variables
+ export LC_ALL=C.UTF-8
+ export LANG=C.UTF-8
+ export PATH=$PATH:/usr/local/lib/
+ export PATH=/usr/local/bin:$PATH
+ export DEBIAN_FRONTEND=noninteractive
+
+
+
+%runscript
+ date
+
+%labels
+ Authors Rachel Legendre, Adrien Pain, Amina Alioua
+ package.name ePeak
+ package.version latest
+ package.homepage https://gitlab.pasteur.fr/hub/ePeak
+ package.license GPLv3
+
diff --git a/config/annotation_config.txt b/config/annotation_config.txt
index 18fa2ae3cb8fc670081045849ef46d99475bc04c..be1768b64816c717f10224c2c06f0dcb7daa1a73 100644
--- a/config/annotation_config.txt
+++ b/config/annotation_config.txt
@@ -7,7 +7,7 @@ skip_lines ^$
theme Gene features
join_type gtf
- target_keys 1,2,3
+ target_keys 1,2,3
reference_file $3
nb_max_results 2
max_dist_nearest_gene 10kb
diff --git a/config/cluster_config.json b/config/cluster_config.json
index 6bcf0b1140b6b0f8a91e6b1b2f4f4f2acafba1b2..61a3fa6b77a241acb228c73abd253b35c5808a49 100644
--- a/config/cluster_config.json
+++ b/config/cluster_config.json
@@ -42,6 +42,11 @@
"computeMatrix" :
{
"ram" : "40G"
- }
+ },
+ "Genrich" :
+ {
+ "ram" : "60G"
+ }
+
}
diff --git a/config/config.yaml b/config/config.yaml
index 3efa018cc00eb69d0412a2a5e045c83385317790..a51089d889932fda870029a06f1d0b5e10a4c6df 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -29,13 +29,13 @@
#=========================================================
# path to the fastq directory
-input_dir: /path/to/raw_data
+input_dir: /path/to/data
# mate pair tag in the fastq filenames (regular expression)
input_mate: '_R[12]'
# filename extension
-input_extension: '.fq'
+input_extension: '.fastq.gz'
# path to the analysis directory
-analysis_dir: /path/to/directory/analysis
+analysis_dir: /path/to/result
# tmpdir: path to temporary directory (default /tmp/, but could be "/local/scratch/")
tmpdir: $TMPDIR
@@ -55,9 +55,9 @@ tmpdir: $TMPDIR
design:
design_file: config/design.txt
- marks: ATAC20
- condition: D0
- replicates: rep
+ marks: H3K27ac, Klf4
+ condition: shCtrl, shUbc9
+ replicates: Rep
spike: no
spike_genome_file: /path/to/genome/directory/dmel9.fa
@@ -74,10 +74,10 @@ design:
#===============================================================================
genome:
- index: yes
- genome_directory: /path/to/genome/directory/
- name: hg38
- fasta_file: /path/to/genome/directory/hg38.fa
+ index: no
+ genome_directory: /path/to/genome/directory/mm10
+ name: mm10
+ fasta_file: /path/to/genome/directory/mm10.fa
#===============================================================================
# FastQC section
@@ -132,7 +132,7 @@ adapters:
bowtie2_mapping:
- options: "-X 2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive "
+ options: "--very-sensitive "
threads: 4
#===============================================================================
@@ -166,7 +166,7 @@ mark_duplicates:
remove_biasedRegions:
do: yes
- bed_file: /path/to/genome/directory/hg38_biasedRegions.bed
+ bed_file: /path/to/genome/directory/mm10-blacklist.v2.bed
threads: 1
#===============================================================================
@@ -231,7 +231,7 @@ seacr:
chipr:
- do: yes
+ do: no
options: "-m 2"
@@ -305,10 +305,10 @@ intersectionApproach:
#===============================================================================
peakAnnotation:
- do: yes
+ do: no
standard: yes
- gtf_file: test/annotation/hg38.gtf
- gene_annotation_file: test/annotation/hg38.txt
+ gtf_file: test/annotation/Mus_musculus.GRCm39.111.gtf
+ gene_annotation_file: test/annotation/Mus_musculus.Ensembl111.txt
config_file: config/annotation_config.txt
@@ -329,7 +329,7 @@ peakAnnotation:
#===============================================================================
differential_analysis:
- do: no
+ do: yes
method: "Limma"
spikes: no
normalisation: "scale"
@@ -371,8 +371,8 @@ bamCoverage:
#===============================================================================
geneBody:
- do: no
- regionsFileName: /path/to/genome/directory/hg38.gtf
+ do: yes
+ regionsFileName: test/annotation/Mus_musculus.GRCm39.111.gtf
threads: 4
#==============================================================================
diff --git a/config/config_atac.yaml b/config/config_atac.yaml
index 0a5382d2aec0181f3776dfc310887bef02a16db8..b19fbd43f5d14be3c4172866d75d02760d1fa1ee 100644
--- a/config/config_atac.yaml
+++ b/config/config_atac.yaml
@@ -27,13 +27,13 @@
#=========================================================
# path to the fastq directory
-input_dir: data_toy
+input_dir: /path/to/data
# mate pair tag in the fastq filenames (regular expression)
-input_mate: '_R[12]'
+input_mate: '_R[12]_001'
# filename extension
-input_extension: '.fq'
+input_extension: '.fastq.gz'
# path to the analysis directory
-analysis_dir: RES/atac/try_8
+analysis_dir: /path/to/results/
# tmpdir: path to temporary directory (default /tmp/, but could be "/local/scratch/")
tmpdir: $TMPDIR
@@ -53,8 +53,8 @@ tmpdir: $TMPDIR
design:
design_file: config/design_atac.txt
- marks: ATAC20
- condition: D0
+ marks: ATAC
+ condition: D0, D6, D6F
replicates: rep
spike: no
spike_genome_file: /path/to/genome/directory/dmel9.fa
@@ -73,9 +73,9 @@ design:
genome:
index: yes
- genome_directory: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38
+ genome_directory: /path/to/genome/directory/hg38
name: hg38
- fasta_file: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.fa
+ fasta_file: /path/to/genome/directory/hg38.fa
#===============================================================================
# FastQC section
@@ -163,7 +163,7 @@ mark_duplicates:
remove_biasedRegions:
do: yes
- bed_file: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_biasedRegions.bed
+ bed_file: /path/to/genome/directory/hg38_biasedRegions.bed
threads: 1
#===============================================================================
@@ -250,7 +250,7 @@ macs3_hmmratac:
genrich:
do: yes
- options: "-j -e M"
+ options: "-j "
#===============================================================================
# Peak calling with LanceOtron, peak-caller dedicated for ATAC-seq, ChIP-seq and
@@ -314,7 +314,7 @@ chipr:
#===============================================================================
intersectionApproach:
- do: yes
+ do: no
nb_min_replicates: 2
min_peak_length: 0
ia_overlap : 0.8
@@ -342,12 +342,13 @@ intersectionApproach:
#===============================================================================
peakAnnotation:
- do: yes
+ do: no
standard: yes
- gtf_file: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.gtf
- gene_annotation_file: data-annot/hg38.txt
+ gtf_file: test/annotation/Mus_musculus.GRCm39.111.gtf
+ gene_annotation_file: test/annotation/Mus_musculus.Ensembl111.txt
config_file: config/annotation_config.txt
+
#===============================================================================
# Compute differential analysis
#
@@ -363,7 +364,7 @@ peakAnnotation:
#===============================================================================
differential_analysis:
- do: no
+ do: yes
method: "Limma"
spikes: no
normalisation: "scale"
diff --git a/config/design_atac.txt b/config/design_atac.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e04c4afc2fd319197a78ede1044b7e80901da8db
--- /dev/null
+++ b/config/design_atac.txt
@@ -0,0 +1,4 @@
+IP_NAME NB_IP
+ATAC_D0 3
+ATAC_D6 3
+ATAC_D6F 3
diff --git a/config/design_noCTL.txt b/config/design_noCTL.txt
old mode 100755
new mode 100644
index 3473020793e31121131537c761b02bc15e9911dc..3279e901df773a51aae33df97d2798ed99fe4ae0
--- a/config/design_noCTL.txt
+++ b/config/design_noCTL.txt
@@ -1,2 +1,6 @@
IP_NAME NB_IP
-ATAC20_D0 3
\ No newline at end of file
+H3K27ac_shCtrl 2
+H3K27ac_shUbc9 2
+Klf4_shCtrl 2
+Klf4_shUbc9 2
+
diff --git a/data-annot/hg38.txt b/data-annot/hg38.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/env.sh b/env.sh
index cae15675a5555236b81b966fdce946024dc665ee..4926565992cf93cac3334373bd54de4d4beda6c7 100644
--- a/env.sh
+++ b/env.sh
@@ -12,3 +12,6 @@ conda install -c bioconda snakemake
conda install -c anaconda pandas
conda install -c bioconda pysam
conda install -c conda-forge singularity
+#mandatory for snakemake 8 only
+pip install snakemake-executor-plugin-slurm
+pip install snakemake-executor-plugin-cluster-generic
\ No newline at end of file
diff --git a/images/epeak_workflow_atac.svg b/images/epeak_workflow_atac.svg
new file mode 100644
index 0000000000000000000000000000000000000000..67c1f18c47786b05ec1d6476c1bed95560c951d7
--- /dev/null
+++ b/images/epeak_workflow_atac.svg
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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
new file mode 100644
index 0000000000000000000000000000000000000000..be94c452804a62d594021c1482bd3d02ef71cbd3
--- /dev/null
+++ b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep1.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0bdeae9a71d468155bca28c3a0777bee0462e837
--- /dev/null
+++ b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep2.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..44c270629dc38a5a823734e6654d659d3bc1d2ed
--- /dev/null
+++ b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D0_rep3.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..4c0b491aad41c52aff043f540d88d507b7390688
--- /dev/null
+++ b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep1.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..7c6c3dc6224268454bf9555e22af2f17a26c8077
--- /dev/null
+++ b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep2.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..81170c98897427a8f50f44bf2ff65edc80ca2359
--- /dev/null
+++ b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6F_rep3.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..3d44b623c7194934feaa25b3e0c86f075398ef63
--- /dev/null
+++ b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep1.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b31b25f73b692fafee6ab1190d1d2964e0b3fdcc
--- /dev/null
+++ b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep2.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..7a9a33f97ccae8eb948539b3f6d23f18942a9f82
--- /dev/null
+++ b/logs/slurm/EstimateLibraryComplexity/EstimateLibraryComplexity_SAMPLE=ATAC_D6_rep3.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..3c40126270c2dcac031c7cfd876db13c50f1f14e
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep1.REF=hg38.err
@@ -0,0 +1,36 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..ef4ec036c11cc0afd790297d29ae71b76984b19e
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep2.REF=hg38.err
@@ -0,0 +1,36 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..dc8c82c4777fc60ed8fcefbf3b71ff5b0b727f9e
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D0_rep3.REF=hg38.err
@@ -0,0 +1,36 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..1a45c1b210cf5bd22a17bd179ebc99fbbc74b8df
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep1.REF=hg38.err
@@ -0,0 +1,36 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..ecd0027c2c64ca01fc0e9acfe4a6f96b7813937d
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep2.REF=hg38.err
@@ -0,0 +1,36 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a94cff3009bbb7d2cd30d9872e7915773c4a14e7
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6F_rep3.REF=hg38.err
@@ -0,0 +1,36 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..739409dedc67de2fbd828874dbecfb1c8976a329
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep1.REF=hg38.err
@@ -0,0 +1,36 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b3988660e2a3e9c4a5424e7cd044a90501adca93
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep2.REF=hg38.err
@@ -0,0 +1,36 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..dffd4c230fd4449fc7aaa7d0460d54a8fdd93e72
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=ATAC_D6_rep3.REF=hg38.err
@@ -0,0 +1,36 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..c62a8e5245fb62a6ed417cf1ef13c49079a777b5
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..24bee8ca4143c60e9d89e201613826a15dd00509
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..1eb284c60390cf35ad55782a62a57fbe1b0c2e78
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..7c2021c523f91cc1c10ad83eabc869a4ff5c9375
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..749020cc89d47969216dae7dab784c5e8f731649
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..aeb4f7e7d0d449651bd419ea6bf6a66398e4271d
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..40ef0e360f7e02e74efebf4606a84742d0c5459b
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..9c0ff81fae15af2694bad74513669874ef7a231e
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a4799c2e9e5dc318b9841e5c98dd7f8a383ec353
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..70ab6531db1a9cd6d9fe67a3693768bc5a9c6b41
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e3e0d06bf92780118d5df5c978c7a973127e8d57
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..54f58242cafdfb1962c1ed5e4115e077a5d99736
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..ee0befb55b2096b590cb8718a3fd8ef8968cc79b
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..04109dd0ddbba36a67922e13d7e2dc79e15ba9e5
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..01d3a745ca569549fea3c5479827c0b9ba844af1
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..d1377ff7366ee348a1cbe17c5a8fd1ff3459c759
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a1430a610d81ceed38bb014274f52982d0612da3
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..a2082f6588d254806207b2c75fadaa495aed8ce3
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..c1e6fe1a8ebcf4c9e060d78872b099557d79805e
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..9aa2bda875d5f97db72b9c636b9b303e098ff91e
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0b9d8f78eb709c3d963ef6f752d7e367c2132e0e
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..a5b0a5cb80885bed498af256aa3624b062b7e9f8
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e9276e832524fdd4a8fd6731c21bc39b99a3db58
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,39 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..ba14d083d5d09aacff5a20eab01cf470ce68b0fe
--- /dev/null
+++ b/logs/slurm/bamCoverage/bamCoverage_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..c0fcf6bba6bfb66f5c214c65547ea4230118e453
--- /dev/null
+++ b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep1.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0dcfcdc884772afd1d5ecdb519819863630653bf
--- /dev/null
+++ b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep2.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..bca35879e4b978c22bf1edee784596c4adc76b0c
--- /dev/null
+++ b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D0_rep3.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..1e9578090e0e9253427c65d886f7f5e14d5f15e0
--- /dev/null
+++ b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep1.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..d13adcbea89dae91bae2508762f3cd124fe34bf3
--- /dev/null
+++ b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep2.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..79a4068c56c167203bdf22609b4775a73dfe0c3c
--- /dev/null
+++ b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6F_rep3.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a090b890b3f75009d16039892a02d15633d0bd61
--- /dev/null
+++ b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep1.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..980b23825f85ca0c5f0109d7cb7505634d4a51be
--- /dev/null
+++ b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep2.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..1265c4f6c120918dbb4839a2419939f19f82ee9b
--- /dev/null
+++ b/logs/slurm/bam_to_bigwig/bam_to_bigwig_SAMPLE=ATAC_D6_rep3.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..7bf832896f586625f193bbfde29089d8b1a5a937
--- /dev/null
+++ b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=genrich.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..44b6315e89dbb1cee3c5ca0ac3edfaf936a67916
--- /dev/null
+++ b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..65fb646f87a66bd9d56bc840f336e2688b2b8abf
--- /dev/null
+++ b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=H3K27ac.err
@@ -0,0 +1,33 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..556c28effdc5cd3c0f04b06caddba2ba636bd21b
--- /dev/null
+++ b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs2_narrow.MARK=Klf4.err
@@ -0,0 +1,33 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..85a32aa4dea925794af22ab9aa403e4d4c8fbf3d
--- /dev/null
+++ b/logs/slurm/bed_to_gff/bed_to_gff_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e7a7aec9c1b9ab436642bcfe8408888fc41ee6e0
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep1.REF=hg38.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..c899ad9d6fc628c58067dc70cdaad12071605bf7
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep2.REF=hg38.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..8da4050524bf841806d8f592af6920d5bb8bcc82
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D0_rep3.REF=hg38.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..037c9946f7bb1f2d996c17a2147cc4af8c05192a
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep1.REF=hg38.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..46b0a6ab36f8558e61035e2c45c1c46eb9a71c17
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep2.REF=hg38.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..020390761e4c1d3cdf0b52aa9793828f273526a0
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6F_rep3.REF=hg38.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..ed0f7a40cd50efdb08fb0c39aed8b34b566f0960
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep1.REF=hg38.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a0509331f5b6ec36427447ac6bfafbb8f20bbbd3
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep2.REF=hg38.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..014fb2e7721d4aabbbef126e97d9dede935d0c57
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=ATAC_D6_rep3.REF=hg38.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a37d98785ad0625c234be2fb5e5b675418ae5a3f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..8934a2591ca5c72e19cf5bc71a1b9323c6739559
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6370f5c6675efa17d38590613eb0622771ff28ad
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..ffa9d68b5343d156c33569f3d61e8c6d1b5f057a
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..87deb993ee7b0db5e7e75502a71b5fabda20b8f6
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..9e5d46b338215d09254cfbf84141690b74b88790
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6874e621cb8dba75c256c6ed52bf93050cb5a610
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..9c2bc1ef98440cb4d40fe6bffd548e4b2e9e9b8b
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..ecfc91dfc0c1cb76ed36b38fc2839ba17872ae66
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..34e7e8806757791facc54c14307ced4535b7b2a4
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..7de24c574c49bb75ee8d1298aa543857934527a0
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..cdbfbec62a9f3d8400fbb0d8f24f9ac3d2cd6f10
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..93f316d7452478aaf1b9af1f89b6b3f1b22190ff
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..789a431514cd255b48fcb2b51252ced5eb314b33
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..d09dbc1d8846e136b712d51cb409469a314ecf43
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..1ba52f266da4bc731e59274f62478b847ea17f71
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..ff937bda09b15a76d3332d6392a6e336f00bb09f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..3e0c3c0ca670ffb12243527ea80fb50bbc6f642e
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..339905dee490e9344eb1a8c8319ad27e56c2422a
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..d5795f91e0164ff86a80e3d92ba590ffc1f1fec3
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b2f467cc63b4aae2acf2a0f5b75a1a7abbfacbcb
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..33d93c71af15cd36745c07a8eb41096dec95e8da
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..ad47acd4e85ea5b27117dec0cf35456af2c7d337
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,58 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..27dbdaf26cb4fabc9acce3e26981d49efd60e83a
--- /dev/null
+++ b/logs/slurm/bowtie2_mapping/bowtie2_mapping_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,58 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..49bf0d3c162af151223b87d9b8bfcd8a750db92e
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,45 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..499c5fbff433111055934f6484f3161d5c629cf1
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=genrich.MOD=narrow.MARK=ATAC.out
@@ -0,0 +1,38 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..0a87d0fe0cd765d9b841add7d920e30d8ca07236
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,45 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..ae9ce67d4847a5d540c84f56072102dae409abe9
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.out
@@ -0,0 +1,38 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..c6d01f96f6d4886dc66b152b887f6979f7519300
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.err
@@ -0,0 +1,75 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..f2f0e3ce03164cbb41c5489ffceff1f90540a9bb
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=H3K27ac.out
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..da4e2488c57d1afec99d2a390d10e89698014a76
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..36d347b7fa4ccdf1e975487a76511c53fd5bb75c
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=macs2_narrow.MARK=Klf4.out
@@ -0,0 +1,38 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..6865148d2c4eb5b8ed77035d4e52ea2a1cbe3261
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err
@@ -0,0 +1,45 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..fbdbf443dbbfd3c0e58b85b1d8e1f961b5e4624d
--- /dev/null
+++ b/logs/slurm/chipflowr/chipflowr_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.out
@@ -0,0 +1,38 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..3a595a54ff1396504fe9010190a9201c3ce2a10f
--- /dev/null
+++ b/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=H3K27ac.err
@@ -0,0 +1,63 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a17840c726f6ec1e3b02c70a5f9bc30ff59c9d0a
--- /dev/null
+++ b/logs/slurm/chipflowr_annotation/chipflowr_annotation_CALLER=macs2_narrow.MARK=Klf4.err
@@ -0,0 +1,63 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..25f003f8ac98b73c8767e7798fdd1fdaf51e56e3
--- /dev/null
+++ b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=genrich.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,26 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b5f092408d316ba5ae25ad09cebb96043f2294bb
--- /dev/null
+++ b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,26 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..c2a8383f4310172121f1c04e4829efc241843171
--- /dev/null
+++ b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=H3K27ac.err
@@ -0,0 +1,28 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..cfb00a34633ce733563a4fe1450a24780e723afc
--- /dev/null
+++ b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs2_narrow.MARK=Klf4.err
@@ -0,0 +1,28 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b14935a3c7f266f789830f8b1bc50ed316aee397
--- /dev/null
+++ b/logs/slurm/chipflowr_init/chipflowr_init_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err
@@ -0,0 +1,26 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b3df6d29cbf3634180f5c714595c206e0b0acf35
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..996d22116dc4e323b3a215fb246cec61316e7107
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..87aedbcf73215ac3c994ce01d34cc86cc9df3871
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=genrich.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..5c68c87963390f877f82a4281743a58f3b188dfd
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D0.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..4ce04d8dc305e18b5472e22af4bd3ca9bba4f10f
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..11e91ee2f3bcef9755549b81b10fe5950e5c31d3
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.IP_NAME=ATAC_D6F.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0ca8cb698d7e75537b3301195824064cb16dc2d7
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shCtrl.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..498546d42366920ee25f623de85418cd2d368b1c
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=H3K27ac.COND=shUbc9.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..40d59f6772967dc74531623acd4d8abeee550930
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shCtrl.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9f69168f5c1f5d1491888d70700181a62f259f85
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=macs2_narrow.MARK=Klf4.COND=shUbc9.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b06a948e4ccd8b064ee1891dd3bec78c209286f4
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D0.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6980cbea13d4a50600f53c3711b0738704d63f3b
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6fcf97fd23d54e8f0ec536061b04ac68f5815af8
--- /dev/null
+++ b/logs/slurm/chipr/chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.IP_NAME=ATAC_D6F.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..49561769e2edc4dcdbe89817209a4833b52c4291
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e234d3a25a3aaa4b7d93f6b1a39928b8c4145929
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e99c02988b98fdebe5daaace10a1cdf85f56dcbd
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..5d08c702737a1a5ac2f74f8c6c1c4ba9da5d71b3
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b2fd2d05178f075638866e8bed1c01322369a8db
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..d48125f389a0275cdde85124fa9744d8b3b14e95
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6f49fdcc49d9b16f85394b89b06b2d6aa33f2681
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..4b2bb0e25d80b3dc926e75433351b9474d44eb8d
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..de871123e6af5ef527ef356e2717732f95772916
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..adc6fafa965af8f3c1df43ed9b097f1d855e394d
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..78970cd81730dbeed0e8ff98d4c6c0044808c5e0
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..034d530650abecc43549c8f82957b5e30108e479
--- /dev/null
+++ b/logs/slurm/computeMatrix/computeMatrix_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..156dfc068e2bcf6a8652eeb822cb031ad46f331c
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=PPR.err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9bb5a4fd35e7766f71e02e05c325ac6a34a881ac
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=Rep.err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..3ad593a5ae95a7f039cf50c9b905a3e3d25a8d3b
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR1..err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..ce5e5a61f9bb6d9369a07777a3485e273dc3d46d
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shCtrl.CASE=SPR2..err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..db3f12b54bba2d4ef172f65fd84f6fcf5e3d20da
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=PPR.err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a328aaa85fcc689b220ff56b667f916b437992d5
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=Rep.err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..81d445b30f9583209f531d27d891985f4bc6c06c
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR1..err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..651a396071c477488cd71b956c3e41763c641bb4
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=H3K27ac_shUbc9.CASE=SPR2..err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..94105abaa67dda7d7de56e72aeadf99fbbc6f2bd
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=PPR.err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..08b4a0c28512ae12db35b37d9dde07002bc6fdd4
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=Rep.err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e6e438aace1e6d51b1f0392e5db8c1357e759998
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR1..err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..5dc8655279766bdded097e36d3bba7d5f7d17980
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shCtrl.CASE=SPR2..err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..5399acbbe8f27432de8a7d7190860471d103063b
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=PPR.err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..1dc12ee936619f115f2b29822a73b2658a19530a
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=Rep.err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..f56337e570d9a673c911c918d603385cd9cf0f0e
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR1..err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9a1557869db6deae5d731b3ef580c4882c15d314
--- /dev/null
+++ b/logs/slurm/compute_idr/compute_idr_IP_IDR=Klf4_shUbc9.CASE=SPR2..err
@@ -0,0 +1,52 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..5884304cff04f64f02fb9b1531b6820f3c70d59c
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep1.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..36eae4c233dc37450329b1ce3df879353ba10f11
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep2.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..e2a51664f721444d519f4edbaf6ec93c7012c0b8
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D0_rep3.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..2e601c1ff745bd4c00df76e0da21596675a7b777
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep1.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..c7dca8502ad003b01e1fbd5dd64d2589c6bf46a2
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep2.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..a44ab04e3504fb202a93d20c679bac349a901f48
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6F_rep3.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..009b83055392b85c1dbb0167dc7280721af2b2e7
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep1.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..8445e80502c03f0f6fd6a8696da9cdb969c7209e
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep2.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..2169de36516862394453e0fcb25db4486d8cebf4
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=ATAC_D6_rep3.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..ebea0418cfecb5c5fe067ddbb7ada410201c78e4
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep1.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..806416deeeb0806fd0991bc74febcc9295b33b7b
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shCtrl_Rep2.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..7d24ea336858c9f2a6480e72cfa77351f3bd3ea5
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep1.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..7adc736ab84b8f1fbceac4f3f1c43bbe7f2086be
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=H3K27ac_shUbc9_Rep2.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..966fe7eb62c9633e458d4f6726b219ba3708c215
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep1.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..31b1196c5962e86ad62d7c31a7e5479a784ce6e1
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shCtrl_Rep2.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..b74c512decc59aa1f43b22d801b491a33edc700d
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep1.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..c9e74972e052a0147c3cb757c4e708ca48bdbda8
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=INPUT_shUbc9_Rep2.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..7d148093bb5f69234a5b2103823d4c81e9e1596c
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep1.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..b664165d6f1c8d21f67a0ec7a9b16ace7708cf32
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shCtrl_Rep2.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..2885a3c2f79a7867f7dbb27fda54c4c568f9c643
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep1.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.err b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..80c06a86c69a70ecb66c88377bcf11b175bb67c3
--- /dev/null
+++ b/logs/slurm/cutadapt/cutadapt_SAMPLE=Klf4_shUbc9_Rep2.err
@@ -0,0 +1,54 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..07f427837166543299a9d6ccd13941b1555dcc24
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep1.err
@@ -0,0 +1,71 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..f47c73b886169cd2ccf64d88b3c48d7079eb11ae
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep2.err
@@ -0,0 +1,71 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..1514eedad2f0fcd654d5162c43fb07f57d1aeb1f
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D0_rep3.err
@@ -0,0 +1,71 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..d468be2ec2e3ac6cc7de9cff09ab9dc05e6c131f
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep1.err
@@ -0,0 +1,71 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..440dc14b10f815f69e188f76ac0d380d0bc857c5
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep2.err
@@ -0,0 +1,71 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..cd702210985a69f0b011d10f6c9ee1c2d847c077
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6F_rep3.err
@@ -0,0 +1,71 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..cce2e7e03f34c7fc2b688174c4098340305b1c81
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep1.err
@@ -0,0 +1,71 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..59447b30523dfe616c68372dcc4974f38c76e74e
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep2.err
@@ -0,0 +1,71 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..97e58f38f51350a6eca6f87a724da9b68c59887d
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=ATAC_D6_rep3.err
@@ -0,0 +1,71 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..da8544f73a9e4e0f3a3ffeca8a5583ab45224262
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep1.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..e77392024caa0fb24dfcc2ad69744bd44890c71d
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shCtrl_Rep2.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..f1df293db551d7751da179339c05b3f6e39680c1
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep1.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..28bf78d2024d804dd62cd752e36f295484bfbc80
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=H3K27ac_shUbc9_Rep2.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..d3c3515fd6eb80f25f7b3dc2be3e255277e07dda
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep1.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..c30716d3eaae6789170f59de9126ec1371658c5e
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shCtrl_Rep2.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..a91cb77e8ccb0326f913ce30c416e84b862902e2
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep1.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..1e831a7237f6080cb61557b8dd5e73e837acd1c1
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=INPUT_shUbc9_Rep2.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..fefffd8f71d473a1292b144496349692a5865c69
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep1.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..d735d03e7967dacea33e72cf87d6674a47ec0141
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shCtrl_Rep2.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.err b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..83e76208f47871dd19a76620e72bc707c90ba655
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep1.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.err b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..b76524e58601fc0239813a44bd1386b055879e47
--- /dev/null
+++ b/logs/slurm/fastqc/fastqc_SAMPLE=Klf4_shUbc9_Rep2.err
@@ -0,0 +1,51 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..773fb2051e2e667fa2481e17fc4c8ab0a70246c1
--- /dev/null
+++ b/logs/slurm/feature_counts/feature_counts_CALLER=genrich.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0e458e08e3b47a94aee5294186eaca583c1ab31c
--- /dev/null
+++ b/logs/slurm/feature_counts/feature_counts_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..db186b0672e4caccdad2602ebc495d380f2f0bed
--- /dev/null
+++ b/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=H3K27ac.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..f7a5b30d2aca2454d3d15f23f94ff3d11893350e
--- /dev/null
+++ b/logs/slurm/feature_counts/feature_counts_CALLER=macs2_narrow.MARK=Klf4.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a91aee65fc530acc28ae5b4dd9035a20969a2d57
--- /dev/null
+++ b/logs/slurm/feature_counts/feature_counts_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..e06aeb2f130db2e549e66fa0688c669c07cfa702
--- /dev/null
+++ b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep1.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..ed5e4a69dfc2da4fcb3f0e29bd9b971f9fdabebb
--- /dev/null
+++ b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep2.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..64a1bae22f382ea613e1d436ae9982357c68dabe
--- /dev/null
+++ b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D0_rep3.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..8df566d88e68723b94a38115982f252a3219c58f
--- /dev/null
+++ b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep1.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..ca8d9cedd8907ec532666600212c4a454e833b90
--- /dev/null
+++ b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep2.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..364de0d1f57100179adfbb727ea860cc0b237aef
--- /dev/null
+++ b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6F_rep3.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..bbc80091b1f167a17056a5acfe2791b13c5b15ee
--- /dev/null
+++ b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep1.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..8cbcd8e8360ad8dd65c1863ddb3e7f0ee2cfb168
--- /dev/null
+++ b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep2.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..3d558164f5373847d6c302d7f146cc75e9dcf2fe
--- /dev/null
+++ b/logs/slurm/genrich/genrich_SAMPLE=ATAC_D6_rep3.err
@@ -0,0 +1,47 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/igv_session/igv_session_unique.err b/logs/slurm/igv_session/igv_session_unique.err
new file mode 100644
index 0000000000000000000000000000000000000000..e25a4899d8dbad3e9e60c09c7f87e4728cb54ff2
--- /dev/null
+++ b/logs/slurm/igv_session/igv_session_unique.err
@@ -0,0 +1,27 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..dd81abb2025fa2ad17414fe42c87fc228e8ae9ce
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=genrich.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..74e8b97da9f327641311fcf480d2a56a0c46eda0
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep1.FORM=narrow.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9113df2ca34cf4596067aa469b19759ae9a6935e
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep2.FORM=narrow.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..be16ce32913987ba8cd15022dbec4a7eff7388cf
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=lanceOtron.MOD=narrow.SAMPLE=ATAC_D0_rep3.FORM=narrow.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9a780065bbd7c0b12da2d737f7b4d430c58a2efe
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep1.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..fa8861b876aaaa4da22a9176b0edc0665251fc37
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CASE=Rep2.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..f7dc4d7a5f98ba88da6d462db67ef1c0dd35ff97
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep1.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9abcb5cc5c0dcfc09008e1a92d967f2b46a975f2
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CASE=Rep2.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..bc3c70fbc37451e84a5a1f1a6cdebfbaa6f2da24
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep1.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..482d4768de60ee803ce2408242d4a7080712a247
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CASE=Rep2.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..7517e545bb04d44b4307b63006c842e062cb4cab
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep1.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..86a3ab3877a1d411a74a8fc534d9c9cad54c7808
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CASE=Rep2.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..7532d34068d9930263e8a520dbeb40b8d20252d7
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep1.FORM=narrow.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9ccb36f4bf725b12e6a3c85cc621393083dd6320
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep2.FORM=narrow.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..bdd8e77bddb5eb3f4df0ee2f3eecbd565ca7602d
--- /dev/null
+++ b/logs/slurm/individualPeakAnnotation/individualPeakAnnotation_CALLER=macs3_CallPeak.MOD=noModel.SAMPLE=ATAC_D0_rep3.FORM=narrow.err
@@ -0,0 +1,55 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..16853132a7817e31b7de1dcc401ad8d88449e813
--- /dev/null
+++ b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep1.REF=hg38.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..d4f3c9b1a06f33c1c9624a319f6f0ab1c272806a
--- /dev/null
+++ b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep2.REF=hg38.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a6d2c01f574bf0a1d731ec0bfd67bca6e96aff19
--- /dev/null
+++ b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D0_rep3.REF=hg38.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..09d928ec6f46ce2ef0a6c13f95ea9b81e56b4046
--- /dev/null
+++ b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep1.REF=hg38.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a0fce253ebd721b47bf52c1fa5ebdd3712f00b98
--- /dev/null
+++ b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep2.REF=hg38.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..4f49d7fdc7593a5741889d7af3b7d704e2611efa
--- /dev/null
+++ b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6F_rep3.REF=hg38.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e8dc4dd4add92ed4feadda5b0de648e2acb828fd
--- /dev/null
+++ b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep1.REF=hg38.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a67ea7d7f9f5c0fa99f7e985fce57fffd69a2434
--- /dev/null
+++ b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep2.REF=hg38.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..2ee80e2a62ea36f40e3c838314bfc45b5e92ee41
--- /dev/null
+++ b/logs/slurm/insert_size_metrics/insert_size_metrics_SAMPLE=ATAC_D6_rep3.REF=hg38.err
@@ -0,0 +1,31 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..c8c73a3a26b7e0fbd78077b51d0e08a9b12dcd65
--- /dev/null
+++ b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..195eeaf15352550b1069ac472553dabe45fb4800
--- /dev/null
+++ b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..f6850a62ec438cc905b68f0d783d0e22c6883d53
--- /dev/null
+++ b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0506951feb09634df8875c83c6f08214c61e0db8
--- /dev/null
+++ b/logs/slurm/intersectionApproach/intersectionApproach_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.err
@@ -0,0 +1,39 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..c3b6fa6849eddc97bfa1b577a8b4135d0dd7eb5f
--- /dev/null
+++ b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep1.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..3d6188e890aa7da50cba9b39c824f7bc6f1a0a13
--- /dev/null
+++ b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep2.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..7c5856a475e3d732a5852b38b7355a997a724dbd
--- /dev/null
+++ b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D0_rep3.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..2e863419b0779a28ab3501c28d9a1c48093297b5
--- /dev/null
+++ b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep1.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..34074f4da2a129531ba1aac917b41faf353d5e20
--- /dev/null
+++ b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep2.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..d0bb8b38ba4273b4db18750b50a80b46115e8f78
--- /dev/null
+++ b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6F_rep3.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..28770ea6aaa1774ad2af9067771c0b7fa24771f0
--- /dev/null
+++ b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep1.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..e628c8192e2e7ef000e596dbc361c49c89105d8a
--- /dev/null
+++ b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep2.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.err b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.err
new file mode 100644
index 0000000000000000000000000000000000000000..af39fad7d5bd42b4f83157e7e38f96d0631640e5
--- /dev/null
+++ b/logs/slurm/lanceotron/lanceotron_SAMPLE=ATAC_D6_rep3.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.err
new file mode 100644
index 0000000000000000000000000000000000000000..bdabfc3f2acad293be03072dcb3e55d4c0dbdc63
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.err
new file mode 100644
index 0000000000000000000000000000000000000000..16c96d83a1c6331f7b3c103b471e428196977cb3
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPR2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.err
new file mode 100644
index 0000000000000000000000000000000000000000..e9221b8d5e021e8cc252a48324b0ac60ccf21597
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_PPRPool.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..b56ddc20dc40e99f3729d8fbe20d2362285d7004
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..12306c3ec5c52ddc6c8f065abd5a48ee74aa3ec9
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_Rep2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.err
new file mode 100644
index 0000000000000000000000000000000000000000..432e1649d186e4843bad7111254006e3671dfc8a
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.err
new file mode 100644
index 0000000000000000000000000000000000000000..41cec468bab3eca63789fffe97ac4c937cb0f8c1
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR1.2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.err
new file mode 100644
index 0000000000000000000000000000000000000000..facfb821057fbb53ea2b7daee53e2852b3406760
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.err
new file mode 100644
index 0000000000000000000000000000000000000000..769f2a18d949a9e8cf03ddd7f1996480285a0dbe
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shCtrl_SPR2.2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.err
new file mode 100644
index 0000000000000000000000000000000000000000..1d62d31aa5ef553c02e5ef585905cc4bfc32156c
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.err
new file mode 100644
index 0000000000000000000000000000000000000000..3c2bd189305f58516f467e570d834dfa24fcfd8a
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPR2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.err
new file mode 100644
index 0000000000000000000000000000000000000000..f33ac7e95859a8ff98f269dc4050651189be8d84
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_PPRPool.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..cb433b73c04c57b5877ddd71e9b3d12f8f2f1a46
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..6a60f0b502e1619bd4fad62e6a4a921f7d1c1966
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_Rep2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.err
new file mode 100644
index 0000000000000000000000000000000000000000..d132c8c5e39430a6c918b95f77c152720b5f3e7e
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.err
new file mode 100644
index 0000000000000000000000000000000000000000..6f11b4ba64d4579f3f122d6d65542c98bdeeb114
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR1.2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.err
new file mode 100644
index 0000000000000000000000000000000000000000..3c5fedc7622d22e622700a5d329562698284ee89
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.err b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.err
new file mode 100644
index 0000000000000000000000000000000000000000..af5fc2c44f7a3f6dd8bd40cb3d3dd843a76c56a2
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=H3K27ac_shUbc9_SPR2.2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.err
new file mode 100644
index 0000000000000000000000000000000000000000..232691e5b7e55c33696f70c155b10ac3b3a7d89b
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.err
new file mode 100644
index 0000000000000000000000000000000000000000..ea9d4422c458cd64c3e9f5b19fa052309ce16147
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPR2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.err
new file mode 100644
index 0000000000000000000000000000000000000000..5c867f26850b5e2d0385be639bda53ad020aa357
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_PPRPool.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..89922c839160ee3107d8684298c1b4c95d8d8dba
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..4383bd40e320a97f860a6d0df62e0a1708b2697b
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_Rep2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.err
new file mode 100644
index 0000000000000000000000000000000000000000..f2bcabcd915d0e0393b456111b331041c3b15480
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.err
new file mode 100644
index 0000000000000000000000000000000000000000..2b15b01e534beb5594db0b7368cc3aa4df67dd64
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR1.2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.err
new file mode 100644
index 0000000000000000000000000000000000000000..b13d466b01b48c5b241c934cd13a3ae78b7781e9
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.err
new file mode 100644
index 0000000000000000000000000000000000000000..01c8c53f8e8d97079b5e3baed39bc890b2bc3cbd
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shCtrl_SPR2.2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.err
new file mode 100644
index 0000000000000000000000000000000000000000..52c0d4b822fe8b154b13ae132df31ad931fdd369
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.err
new file mode 100644
index 0000000000000000000000000000000000000000..3e9bb5060b4514696df40791029deed17dd2d0ef
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPR2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.err
new file mode 100644
index 0000000000000000000000000000000000000000..c36ab541eaeebb2953665dfb2652ee3eae6c3d65
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_PPRPool.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..a1514872126b5a05d3e05199c6987d46da64b77d
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..3301242ec4a44179253cbfc29ccfdba72d03c8ee
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_Rep2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.err
new file mode 100644
index 0000000000000000000000000000000000000000..bada02cb1ee7a41379dfdc4e234c6e71bf70a7ac
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.err
new file mode 100644
index 0000000000000000000000000000000000000000..9bcf9dfef959f751c57486d65463a498848ef225
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR1.2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.err
new file mode 100644
index 0000000000000000000000000000000000000000..293dbd5656136dc3d5c4a9c9044707fc150872a7
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.1.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.err b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.err
new file mode 100644
index 0000000000000000000000000000000000000000..3f7903db4b061e6854ea4a3f20daf06ead0b17c7
--- /dev/null
+++ b/logs/slurm/macs2/macs2_SAMPLE=Klf4_shUbc9_SPR2.2.err
@@ -0,0 +1,49 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..429123afdd2a8791d20c92956d354314b042e12a
--- /dev/null
+++ b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep1.err
@@ -0,0 +1,53 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e508280804834e0c2a96f0923ce6b670c6d25416
--- /dev/null
+++ b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep2.err
@@ -0,0 +1,53 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..5729ce9dae15aba014464d2cbb48a961d81d690d
--- /dev/null
+++ b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D0_rep3.err
@@ -0,0 +1,53 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0e2f100b0f75ade8b5275669ef2ddef96fa7a8f2
--- /dev/null
+++ b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep1.err
@@ -0,0 +1,53 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..64ee511775c4bbadc0262c6e20c3031017de77fe
--- /dev/null
+++ b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep2.err
@@ -0,0 +1,53 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..1700a92eaece1128497beed12370119e3467d3ec
--- /dev/null
+++ b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6F_rep3.err
@@ -0,0 +1,53 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..2d03ac7f2935cb97dbf603a8aba0096dd180cbcb
--- /dev/null
+++ b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep1.err
@@ -0,0 +1,53 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..4443406ffbe93b8d3cf9e9fbf33c3a89f5d93d30
--- /dev/null
+++ b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep2.err
@@ -0,0 +1,53 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..08a6251a03b767aa8acda840c668ff9f8d0dfb37
--- /dev/null
+++ b/logs/slurm/macs3_CallPeaks/macs3_CallPeaks_SAMPLE=ATAC_D6_rep3.err
@@ -0,0 +1,53 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..17fe60191387bc5c47be1b8dc87fa9d1312c9878
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep1.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..bb8561e495d9c3a1a012ac1f3836f59666e10bc8
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep2.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..601052255d95929222df03da45e95e12098fbb27
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D0_rep3.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..26310c447b6bc30a8cbe07a29a9af04582819c4e
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep1.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6ff9ef280a2f664c51a548b7df49c0fd1dd1fa44
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep2.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..80578a13f85d11cf8c3ac0e29c45039e1aabdfb5
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6F_rep3.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..3facf5e963b4342cbfa2244d6832ce46a8f3f39c
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep1.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..2b375e01fa0d3b7a3f3a482e51ec67ee345c94d2
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep2.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0a99a961a48397eba82d05a366823c0e8afad534
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=ATAC_D6_rep3.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..cfe548232c4aa2593f64798720a641ac5fe90a2a
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..e8811b7198789863933238b8eeffffc15fc1d941
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6b30bfd70b2b5cc26a20b69bfbbf0ff6bae85994
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..7657e9d3cce6f6cfd19d30fda89f3ed5d4ca63e4
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..07cae2e4f692ef5fc5dca89d460c5c6bf9948182
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..6b058e3d300f745c7c95848014eb101dcc6babb3
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..358bbbd3d8da6acbaa1fa8c924ea409ba973349a
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..aa0d6591af237e8da73a1a3a2512273906e13202
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6851cc4d5eabe3b8f4b15169d80033fb473d33ec
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..538390fad9b92c01fcbf2dcab387c5f448d62fed
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..fddaf8758351aab5bd61ebb7573d4f4d32de6af7
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..b981b989514db18f11f90a01e4bcd2797cf25196
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..bd87e4cacf53ddc88e9d6dd573b1372292cd6f8e
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..c43beb989b044d7199310bc610165e9092e8c537
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b887f1b20b2036b5801a0876b6e892ac84e68815
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..eb37e20ca438efc3cf4a54fb00990227b1414395
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9bc989b76d2dc5ea69caef250b8e8e09ef772ce0
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..d8a380e6060c8c966ae4a6d41666aa60d0f11d55
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e59e46fba0b1324940d2f01f72abf6b0517fc4eb
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..7879798a784734f80c6d7efcd050b6d0fd1b33e0
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..74ac7b2b1fd6dfb7942b6dec9e9de679513271e8
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..12ce8aa4c8bb2c4e959fc1d102abbbf044d9af1b
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6d614655ab7a2a066c17ca18ed539703ac268cf8
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..3b2315ed5ff4d7d4bccdf7dfa5029a5ad34b3e1f
--- /dev/null
+++ b/logs/slurm/mark_duplicates/mark_duplicates_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..82d227fab9d0257ef3c75aed98e9e997c9b2c61c
--- /dev/null
+++ b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep1.FORM=narrow.err
@@ -0,0 +1,40 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..709fd4bdce1330cd00d251c356c8d6e9d38ed8c1
--- /dev/null
+++ b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep2.FORM=narrow.err
@@ -0,0 +1,40 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..4d7a078711b3c53428564af300ce176e6fcced0f
--- /dev/null
+++ b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D0_rep3.FORM=narrow.err
@@ -0,0 +1,40 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..6fafbfe4b3ae81ad774728524c065eff05339947
--- /dev/null
+++ b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep1.FORM=narrow.err
@@ -0,0 +1,40 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..33021fcb3483b9babd4004624fa0cd93096b9fae
--- /dev/null
+++ b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep2.FORM=narrow.err
@@ -0,0 +1,40 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b851bee5eea9d537c50954152b3a97009572631b
--- /dev/null
+++ b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6F_rep3.FORM=narrow.err
@@ -0,0 +1,40 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..17805f1085454ae041459a8da005b3c17b3aa74a
--- /dev/null
+++ b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep1.FORM=narrow.err
@@ -0,0 +1,40 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..19bb7b2a0a6be35fc6ac6352f69f10e29f7d13c1
--- /dev/null
+++ b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep2.FORM=narrow.err
@@ -0,0 +1,40 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a8ad5e9b72dc6ca363e90ac95fa7bbcf8dedda13
--- /dev/null
+++ b/logs/slurm/merge_peakcaller/merge_peakcaller_SAMPLE=ATAC_D6_rep3.FORM=narrow.err
@@ -0,0 +1,40 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..672745fb3d032d8b64bcb5042e55985ff885869c
--- /dev/null
+++ b/logs/slurm/metrics_chipr/metrics_chipr_CALLER=genrich.MOD=narrow.FORM=narrow.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..781587859604002bd2df0144787fe021b1e9c213
--- /dev/null
+++ b/logs/slurm/metrics_chipr/metrics_chipr_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..2dc1e97bc9632f18f756ba44e9c911e73e9780b4
--- /dev/null
+++ b/logs/slurm/metrics_chipr/metrics_chipr_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/metrics_chipr/metrics_chipr_unique.err b/logs/slurm/metrics_chipr/metrics_chipr_unique.err
new file mode 100644
index 0000000000000000000000000000000000000000..f583d61efa529480f7f799beb07b799d1f43f6d2
--- /dev/null
+++ b/logs/slurm/metrics_chipr/metrics_chipr_unique.err
@@ -0,0 +1,26 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/metrics_peaks/metrics_peaks_unique.err b/logs/slurm/metrics_peaks/metrics_peaks_unique.err
new file mode 100644
index 0000000000000000000000000000000000000000..dda107f477fab3c638c03528a072733a94206d9a
--- /dev/null
+++ b/logs/slurm/metrics_peaks/metrics_peaks_unique.err
@@ -0,0 +1,27 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/multiqc/multiqc_unique.err b/logs/slurm/multiqc/multiqc_unique.err
new file mode 100644
index 0000000000000000000000000000000000000000..bcd14d14d893bdedebfe49d707a76681885f62de
--- /dev/null
+++ b/logs/slurm/multiqc/multiqc_unique.err
@@ -0,0 +1,29 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..864f314327d8277eb6b80b4621a25f2c2886f5b6
--- /dev/null
+++ b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep1.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..2af1f1ae39cc5eb97678b3e63c8d4b5b5e10fbe2
--- /dev/null
+++ b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shCtrl_Rep2.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..0cca8d63980bf72f04cd59b3d27c83e7ae8daf06
--- /dev/null
+++ b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep1.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..5bd0703ec2f129ecc93a6c02b72fb9a9dcd074b7
--- /dev/null
+++ b/logs/slurm/plotFingerprint/plotFingerprint_IP=H3K27ac_shUbc9_Rep2.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..128af95031dca4f2cf22eae6d881c8f264ae2629
--- /dev/null
+++ b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep1.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..bf0171c9c0c52019ba31791a96b6897a136dfc1c
--- /dev/null
+++ b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shCtrl_Rep2.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..49b8842da2450ada37b4777a8f398cdef8eb3e0c
--- /dev/null
+++ b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep1.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.err b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..9702dee165580bd7346559f9b4ebfdabbec455a4
--- /dev/null
+++ b/logs/slurm/plotFingerprint/plotFingerprint_IP=Klf4_shUbc9_Rep2.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..789a10477555962de7b3e4f5471ec42fcb4e3165
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..2ed008e9a96acb85ef34fb248910df784c0c18f3
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..386e48b5bf5b92d1e6acc2e715552aefb375fcfe
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b8a365120c7cef63dd03d8110e0bfc9f7693ee7e
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..8f4caca664d538540dd681b0531cc0b40a9ed34e
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e7890e7d1c7c17b1824967a0ebd56f1f32f6c6c9
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..48c2ba3cdf1cff034ac6dfc6e9168a675504d048
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..583902a0120531295619deb77e048ba1e7c120d1
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e3cfb09392209f0eab4a2f09e8bbacb7093b7982
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..be03f8bef69826e73f0011aeb19b749bd2530c68
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..8698ff1e3f42127da5cc008a032042d0890a9ae5
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b438c61a6f9b65edcb765bc6e32e91536c4dcf9b
--- /dev/null
+++ b/logs/slurm/plotHeatmap/plotHeatmap_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.err b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.err
new file mode 100644
index 0000000000000000000000000000000000000000..7f2b5f9f2d8074dd8b8831e1a13da12f0d2f113f
--- /dev/null
+++ b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shCtrl.err
@@ -0,0 +1,152 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.err b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.err
new file mode 100644
index 0000000000000000000000000000000000000000..5bd8bb67643a3f589dcce42a00f29a0aa401b70a
--- /dev/null
+++ b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=H3K27ac_shUbc9.err
@@ -0,0 +1,152 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.err b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.err
new file mode 100644
index 0000000000000000000000000000000000000000..b47651ac687446003c42315ef4d190b9bfeed134
--- /dev/null
+++ b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shCtrl.err
@@ -0,0 +1,152 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.err b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.err
new file mode 100644
index 0000000000000000000000000000000000000000..b761fee6cac3f95ae70006d4e09453ca77296239
--- /dev/null
+++ b/logs/slurm/preIDR_PPR/preIDR_PPR_IP=Klf4_shUbc9.err
@@ -0,0 +1,152 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.err b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.err
new file mode 100644
index 0000000000000000000000000000000000000000..4d65f708bf51076a5a5d5a4e3b11115b00f0956b
--- /dev/null
+++ b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shCtrl.err
@@ -0,0 +1,161 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.err b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.err
new file mode 100644
index 0000000000000000000000000000000000000000..264b02ecf4acb4b7e6c70381c94082498f71c72e
--- /dev/null
+++ b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=H3K27ac_shUbc9.err
@@ -0,0 +1,161 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.err b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.err
new file mode 100644
index 0000000000000000000000000000000000000000..228b446f2b7866cc2042c0e880b9b17c83c7aca1
--- /dev/null
+++ b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shCtrl.err
@@ -0,0 +1,161 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.err b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.err
new file mode 100644
index 0000000000000000000000000000000000000000..13ba74094c2a8db0305c6c5d1bef21a5831cf458
--- /dev/null
+++ b/logs/slurm/preIDR_SPR/preIDR_SPR_IP=Klf4_shUbc9.err
@@ -0,0 +1,161 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0b1b7e19cc5ceb17dbe36162b5a04a80c179ae68
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep1.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a773013611d8e2dc136aa3664f255b58645f1fa1
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep2.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..2a8c852f69010662981dea844b6ee62bece592a8
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D0_rep3.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..3928254d5e87998fd3dccd95896d267804ad51da
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep1.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..8f1959bc0f93d8f495c2ad067722ac7932a766d5
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep2.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..359eabae97e6260e93bd3caa467c93be6e596f05
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6F_rep3.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..a445d77e39186c98b2b9b047e7b116bf1ce7d1fa
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep1.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..300c777c451d4719df5a44a048d7fba732e9f100
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep2.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..13bf7e0d6ed7613a06a35b672778ebd90f455773
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=ATAC_D6_rep3.REF=hg38.err
@@ -0,0 +1,30 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e81959fd2795c3c45f0a6a3efc8b5acc474e1a83
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..d6eb724db29eae90c465605047c01df98fe18291
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..845b38cf9f57986df36dfebf6ad68766a01253e8
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..7bab108c6ec841495bf6a7a0695f3b852546116f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e9e57ba1c7f3300c6e619fe6c74b09bcc19c16b2
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..194a6d40d771aa12fc4ad06d0341612a0da5ae85
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e1017bd6d0c1b52b2bee56b6e8514d2f2154c007
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..3469839405233d751c320ed795dc4947a0b01e57
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=H3K27ac_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b3049ec7df32047a48fa12f41443074db1b7d8ee
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..0c7785841c462713cdd81d9d42ba4d53a38ba491
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0efe08d6ffd018f30c7949040e558f1fe0dc47e6
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..31dc03328515bcd192cb221ebd7c3d62b817b265
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..2da87236b390a01af0f51e1ead5ed6861f04eced
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..3cf607fa7969e73f9c29e560a853da05c1efb421
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9a7d168da5cc75471fe1afd162c25d7b53609e28
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..5fae6a4080cc59995aaaede93b81984aca066270
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=INPUT_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b2a681d1f721945507dc0c1866d257f00ca50aac
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..068746d1babb0df0f1a2946aec7f5300d2f3bd71
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9f313e7a70ab0764d0b871d83c73eac6c56cdd77
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..45aff0d78e28401d95a90da6c4d3e008f09ab594
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shCtrl_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..973218b87cf248ba97ca6777bbb105d877449070
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..e3dce91c8f62a0418c86dfc6fdff027359dabb46
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep1.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..8e4d845f1c9d1b55c6cf5a1d8eaad13708cd17df
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.err
@@ -0,0 +1,32 @@
+/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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfbf08886fca9a91cb753ec8734c84fcbe52c9f
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=hg38.out
@@ -0,0 +1 @@
+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
new file mode 100644
index 0000000000000000000000000000000000000000..cc7effbe1e58abdd1d210ff4532ed94705cbd8bf
--- /dev/null
+++ b/logs/slurm/remove_biasedRegions/remove_biasedRegions_SAMPLE=Klf4_shUbc9_Rep2.REF=mm10.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..b01318e8312f5d9f4266466c710b6cc057b1e612
--- /dev/null
+++ b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=IA.bed.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..9f4496a7fc18ae4f4760897c95e9a8903ec2c3bd
--- /dev/null
+++ b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shCtrl.CONSENSUS_MOD=select.narrowPeak.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..d837738ff5f955ba11fef7b3bb1a60c65fd915b7
--- /dev/null
+++ b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=H3K27ac_shUbc9.CONSENSUS_MOD=select.narrowPeak.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..f3fa866fdf97f0c61dc584208da7180b88ca2b24
--- /dev/null
+++ b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shCtrl.CONSENSUS_MOD=select.narrowPeak.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..ac5d5321a8d6a7fa62fc442e02eae3ee89c60d52
--- /dev/null
+++ b/logs/slurm/reproduciblePeakAnnotation/reproduciblePeakAnnotation_CALLER=macs2_narrow.IP_IDR=Klf4_shUbc9.CONSENSUS_MOD=select.narrowPeak.err
@@ -0,0 +1,61 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..3db34c69b2fcb01b9cd10e19043a5f490621d28a
--- /dev/null
+++ b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shCtrl.err
@@ -0,0 +1,35 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..3eb9143707c363d13c4a43fb5e5e18cd828d9473
--- /dev/null
+++ b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..9a099f9e71b88cb61581276fa58f6ae43c860705
--- /dev/null
+++ b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=H3K27ac_shUbc9.out
@@ -0,0 +1 @@
+['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
new file mode 100644
index 0000000000000000000000000000000000000000..1f62e641d5feccc6872021959dd89da29d3bc147
--- /dev/null
+++ b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..9a099f9e71b88cb61581276fa58f6ae43c860705
--- /dev/null
+++ b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shCtrl.out
@@ -0,0 +1 @@
+['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
new file mode 100644
index 0000000000000000000000000000000000000000..81b491ab78b5b49afc50651d7f6ffd7d759e642f
--- /dev/null
+++ b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.err
@@ -0,0 +1,41 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..9a099f9e71b88cb61581276fa58f6ae43c860705
--- /dev/null
+++ b/logs/slurm/select_peaks/select_peaks_CALLER=macs2.IP_IDR=Klf4_shUbc9.out
@@ -0,0 +1 @@
+['shCtrl', 'shUbc9']
diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.err b/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..cbbfd12a27496f83d94cecf60adc2034df07928d
--- /dev/null
+++ b/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep1.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.err b/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..e9b668a7187938010e4dbb1d89df67db4e6e81da
--- /dev/null
+++ b/logs/slurm/spp/spp_ALL=H3K27ac_shCtrl_Rep2.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.err b/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..26c59de27f19282f4821345f17b0524ed74754b1
--- /dev/null
+++ b/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep1.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.err b/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..d744b283e9d36922051572d2d9c7e50b34dc44d3
--- /dev/null
+++ b/logs/slurm/spp/spp_ALL=H3K27ac_shUbc9_Rep2.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.err b/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..901a6e0517baf3e4f98a1250abcef48b3c890642
--- /dev/null
+++ b/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep1.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.err b/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..0c38c3d7f61eb00311079cc447fe725e351896c6
--- /dev/null
+++ b/logs/slurm/spp/spp_ALL=Klf4_shCtrl_Rep2.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.err b/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.err
new file mode 100644
index 0000000000000000000000000000000000000000..547cf865c6edea7850affa58517d1ecfc501ea22
--- /dev/null
+++ b/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep1.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.err b/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.err
new file mode 100644
index 0000000000000000000000000000000000000000..e75d0f48eb27591baf3f8f2335f19c117159e550
--- /dev/null
+++ b/logs/slurm/spp/spp_ALL=Klf4_shUbc9_Rep2.err
@@ -0,0 +1,32 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/logs/slurm/stats_IA/stats_IA_unique.err b/logs/slurm/stats_IA/stats_IA_unique.err
new file mode 100644
index 0000000000000000000000000000000000000000..6f4f6d4571a6e56022e8aa059ce5b80c6e91508f
--- /dev/null
+++ b/logs/slurm/stats_IA/stats_IA_unique.err
@@ -0,0 +1,27 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0ad8e7abf6a8a74626a8d188fc4aa0159015187a
--- /dev/null
+++ b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=genrich.MOD=narrow.FORM=narrow.err
@@ -0,0 +1,26 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..39691c7e95455ba1eba09047f1dd8ffbba3a4ee0
--- /dev/null
+++ b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=lanceOtron.MOD=narrow.FORM=narrow.err
@@ -0,0 +1,26 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..0cfefe83335e940b2a868b763e73ee9f823722b0
--- /dev/null
+++ b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs2.MOD=narrow.err
@@ -0,0 +1,28 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..4094277d3fb3ee1e0d7257ed477bf4c6b676c69b
--- /dev/null
+++ b/logs/slurm/stats_peakCalling/stats_peakCalling_CALLER=macs3_CallPeak.MOD=noModel.FORM=narrow.err
@@ -0,0 +1,26 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..5d9b4cf086275e7209adc8ef9372ed0ca2317fac
--- /dev/null
+++ b/logs/slurm/union_peaks/union_peaks_CALLER=genrich.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..7cb00d5d9a07084610b09b25e6ed342fd939fbd8
--- /dev/null
+++ b/logs/slurm/union_peaks/union_peaks_CALLER=lanceOtron.MOD=narrow.MARK=ATAC.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..06cd73078c7f39a2e59cafe5c5888f8a72ade18a
--- /dev/null
+++ b/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=H3K27ac.err
@@ -0,0 +1,38 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..d41e811b1e292c5442b22e1097fc4a4924feba8a
--- /dev/null
+++ b/logs/slurm/union_peaks/union_peaks_CALLER=macs2_narrow.MARK=Klf4.err
@@ -0,0 +1,38 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/Snakefile:384: SyntaxWarning: invalid escape sequence '\.'
+ POOL = "[A-Za-z-_0-9]+_PPRPool",
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ # if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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
new file mode 100644
index 0000000000000000000000000000000000000000..e5d5c5c0c21b9887e9655d8948fc3b6500bf4568
--- /dev/null
+++ b/logs/slurm/union_peaks/union_peaks_CALLER=macs3_CallPeak.MOD=noModel.MARK=ATAC.err
@@ -0,0 +1,35 @@
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:62: SyntaxWarning: invalid escape sequence '\/'
+ rep.append(sample.split("_")[2])
+/pasteur/zeus/projets/p01/BioIT/Rachelbis/epeak/workflow/rules_atac/chipflowr_init.rules:64: SyntaxWarning: invalid escape sequence '\/'
+ #if spikes, read json file
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled 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
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/profile/__pycache__/CookieCutter.cpython-312.pyc b/profile/__pycache__/CookieCutter.cpython-312.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..4f2f6d397f48e1b65b53474172ee89dab0ec7407
Binary files /dev/null and b/profile/__pycache__/CookieCutter.cpython-312.pyc differ
diff --git a/profile/__pycache__/slurm_utils.cpython-312.pyc b/profile/__pycache__/slurm_utils.cpython-312.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..999c8ce8f59f66351f92e99dfa7b9a1033d2c82a
Binary files /dev/null and b/profile/__pycache__/slurm_utils.cpython-312.pyc differ
diff --git a/profile/config.yaml b/profile/config.yaml
index a5f201128266e76f99a8e0aaf3bdfc9a2b832ec8..13efe1fe0a3fbd2bfb83ae9c863dd1f22bf7b7aa 100644
--- a/profile/config.yaml
+++ b/profile/config.yaml
@@ -35,6 +35,9 @@ cores: 1
#configfile: config/config_atac.yaml
#jobname: "{rule}__{jobid}"
#benchmark-extended: "True"
+apptainer-prefix: "/pasteur/zeus/projets/p01/BioIT/Rachelbis/"
+apptainer-args: "-B /pasteur/"
+
# ================================================= #
diff --git a/profile_v7/config.yaml b/profile_v7/config.yaml
index e35510d20fcb7f13f7e929fa228d3217465c9a62..46853f40e1c4abd3b2f5d4cb3948ec209ff3f94c 100755
--- a/profile_v7/config.yaml
+++ b/profile_v7/config.yaml
@@ -31,7 +31,7 @@ rerun-incomplete: "True"
nolock: "True"
dry-run: "False"
cores: 1
-configfile: config/config_at.yaml
+configfile: config/config_atac.yaml
#use-apptainer: "True"
# ================================================= #
@@ -80,7 +80,8 @@ set-resources:
- computeMatrix:mem_mb=40G
- java_hmmratac:mem_mb=60G
- avatar:mem_mb=30G
+ - genrich:mem_mb=60G
#- avatar: slurm_partition: "gpu"
-# ================================================= #
\ No newline at end of file
+# ================================================= #
diff --git a/test/annotation/Annotation - readme.pdf b/test/annotation/Annotation-readme.pdf
similarity index 100%
rename from test/annotation/Annotation - readme.pdf
rename to test/annotation/Annotation-readme.pdf
diff --git a/workflow/rules/EstimateLibraryComplexity.rules b/workflow/rules/EstimateLibraryComplexity.rules
index 2cc0f89fdf4722564ef17a4560c8c41e43488d90..d1587bc2000401151f6aaa7a3e0df160f3a58ee1 100755
--- a/workflow/rules/EstimateLibraryComplexity.rules
+++ b/workflow/rules/EstimateLibraryComplexity.rules
@@ -29,7 +29,7 @@ rule EstimateLibraryComplexity:
output:
metrics = lib_complexity_metrics
singularity:
- "epeak.img"
+ "epeak.sif"
log:
out = lib_complexity_log_std,
err = lib_complexity_log_err
diff --git a/workflow/rules/bamCoverage.rules b/workflow/rules/bamCoverage.rules
index d4de83ae32b9485e4b3d952de9b6618d02f29c8e..514d66ef351511fa9ed41650cacc0cec39436da3 100755
--- a/workflow/rules/bamCoverage.rules
+++ b/workflow/rules/bamCoverage.rules
@@ -31,7 +31,7 @@ rule bamCoverage:
output:
bamCoverage_output
singularity:
- "epeak.img"
+ "epeak.sif"
params:
options = bamCoverage_options
envmodules:
diff --git a/workflow/rules/bed_to_gff.rules b/workflow/rules/bed_to_gff.rules
index 35c9f7c575250fbdd9b3250e5c2db1cb9b575819..310bf146cda787dd9b4567d3a2960a03557de503 100755
--- a/workflow/rules/bed_to_gff.rules
+++ b/workflow/rules/bed_to_gff.rules
@@ -31,7 +31,7 @@ rule bed_to_gff:
output:
temp(bed_to_gff_output)
singularity:
- "epeak.img"
+ "epeak.sif"
shell:
"""
awk 'BEGIN{{OFS="\t"}} {{print $1"\tChIPflow\tpeak\t"$2+1"\t"$3+1"\t.\t.\t.\tgene_id \"$1"_"$2"_"$3}}' {input} > {output} 2> {log.out}
diff --git a/workflow/rules/bedgraph.rules b/workflow/rules/bedgraph.rules
index c7068b560d48ccc954039d3d23e3a6a6e87880b3..bc511c15161ab9567302a975a242ea9adb0b2015 100755
--- a/workflow/rules/bedgraph.rules
+++ b/workflow/rules/bedgraph.rules
@@ -32,7 +32,7 @@ rule bedgraph:
genome = bedgraph_genome,
options = bedgraph_options
singularity:
- "epeak.img"
+ "epeak.sif"
log:
out = bedgraph_logs
shell:
diff --git a/workflow/rules/bowtie2_index.rules b/workflow/rules/bowtie2_index.rules
index a47fa4d2ae611a991f450c8e7c00508032d5c870..539e07eabaf12063741f32709725a935da1594e9 100755
--- a/workflow/rules/bowtie2_index.rules
+++ b/workflow/rules/bowtie2_index.rules
@@ -28,8 +28,8 @@ rule bowtie2_index:
fasta = bowtie2_index_fasta
output:
bowtie2_index_output_done
- #singularity:
- # "epeak.img"
+ singularity:
+ "epeak.sif"
params:
prefix = bowtie2_index_output_prefix
log:
diff --git a/workflow/rules/bowtie2_mapping.rules b/workflow/rules/bowtie2_mapping.rules
index a65929d2ccccadc4dde4b3fe07938a3c376063ec..868d508ae1aed06f3d58e3bdeac064c0e50d17cf 100755
--- a/workflow/rules/bowtie2_mapping.rules
+++ b/workflow/rules/bowtie2_mapping.rules
@@ -31,7 +31,7 @@ rule bowtie2_mapping:
sort = bowtie2_mapping_sort,
bam = temp(bowtie2_mapping_bam)
singularity:
- "epeak.img"
+ "epeak.sif"
log:
err = bowtie2_mapping_logs_err,
out = bowtie2_mapping_logs_out
diff --git a/workflow/rules/chipflowr.rules b/workflow/rules/chipflowr.rules
index 339916e67f53da822fb0c06dc91e964b63ca361d..c47807e9aa5686d7709c302e82374acba26f54dd 100755
--- a/workflow/rules/chipflowr.rules
+++ b/workflow/rules/chipflowr.rules
@@ -33,7 +33,7 @@ rule chipflowr:
log:
out = chipflowr_logs
singularity:
- "epeak.img"
+ "epeak.sif"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/chipflowr_annotation.rules b/workflow/rules/chipflowr_annotation.rules
index 8107b1aa45a3b07aa93994be6522b4c83fb852f2..bd1028e6d5dcec145df8bd1cc6cc740b6da67584 100644
--- a/workflow/rules/chipflowr_annotation.rules
+++ b/workflow/rules/chipflowr_annotation.rules
@@ -23,33 +23,30 @@
rule chipflowr_annotation:
-# RAF : inclure la librairie bx dans l'image singularity
-# singularity:
-# "epeak.img"
input:
diffannot_input_dir
-
- log:
- diffannot_logs
-
output:
- directory(diffannot_output_dir)
-
+ dir = directory(diffannot_output_dir),
+ done = diffannot_output_done
params:
gtf_file=config['peakAnnotation']['gtf_file'],
- standard_annotation=config['peakAnnotation']['standard'],
+ standard_annotation=config['peakAnnotation']['standard'],
gene_annotation_file=config['peakAnnotation']['gene_annotation_file'],
annotation_config=config['peakAnnotation']['config_file']
-
+ log:
+ diffannot_logs
+ singularity:
+ "epeak.sif"
shell:
"""
set +o pipefail
- if [ "{params.standard_annotation}" = "True" ]
- then
- sh workflow/scripts/annote_analysis_diff.sh {params.gtf_file} {params.gene_annotation_file} `dirname {input}` >{log} 2>&1
- else
- sh workflow/scripts/annote_analysis_diff.sh {params.annotation_config} `dirname {input}` >{log} 2>&1
- fi
-
+ if [ "{params.standard_annotation}" = "True" ]
+ then
+ sh workflow/scripts/annote_analysis_diff.sh {params.gtf_file} {params.gene_annotation_file} `dirname {input}` >{log} 2>&1
+ else
+ sh workflow/scripts/annote_analysis_diff.sh {params.annotation_config} `dirname {input}` >{log} 2>&1
+ fi
+ touch {output.done}
"""
+
diff --git a/workflow/rules/chipflowr_init.rules b/workflow/rules/chipflowr_init.rules
index f3efb1cc0ec7eb529165c8dd01cac7e2c88952c9..964698051ffe372a5972c860decb7faffbc5e0e7 100755
--- a/workflow/rules/chipflowr_init.rules
+++ b/workflow/rules/chipflowr_init.rules
@@ -27,6 +27,8 @@ rule chipflowr_init:
input:
matrix = chipflowr_init_input,
done = chipflowr_init_input_done
+ output:
+ config = chipflowr_init_config_r
params:
conds = chipflowr_init_conds,
rep = chipflowr_init_rep,
@@ -38,9 +40,6 @@ rule chipflowr_init:
batch = chipflowr_init_batch,
genome = chipflowr_init_genome,
outdir = chipflowr_init_output_dir
-
- output:
- config = chipflowr_init_config_r
run:
import os
import linecache
@@ -50,9 +49,9 @@ rule chipflowr_init:
cwd = os.getcwd()
# Sed on matrix to get MARK_COND_REP as sample names
if 'NobiasedRegions' in open(input.matrix).read():
- shell("sed -i -E 's/((\/[A-Za-z0-9._-]+){{0,}})(\/04-NobiasedRegions\/)//g' %s && sed -i 's/_%s_sort_dedup_biasedRegions.bam//g' %s" % (input.matrix, params.genome, input.matrix))
+ shell("sed -i -E 's/((\/?[A-Za-z0-9._-]+){{0,}})(\/04-NobiasedRegions\/)//g' %s && sed -i 's/_%s_sort_dedup_biasedRegions.bam//g' %s" % (input.matrix, params.genome, input.matrix))
elif 'Deduplication' in open(input.matrix).read():
- shell("sed -i -E 's/((\/[A-Za-z0-9._-]+){{0,}})(\/03-Deduplication\/)//g' %s && sed -i 's/_%s_sort_dedup.bam//g' %s " % (input.matrix, params.genome, input.matrix))
+ shell("sed -i -E 's/((\/?[A-Za-z0-9._-]+){{0,}})(\/03-Deduplication\/)//g' %s && sed -i 's/_%s_sort_dedup.bam//g' %s " % (input.matrix, params.genome, input.matrix))
# get cond and rep vectors
samples = (linecache.getline(input.matrix, 2)).rstrip().split('\t')[6:]
@@ -62,7 +61,7 @@ rule chipflowr_init:
conds.append(sample.split("_")[1])
rep.append(sample.split("_")[2])
- #if spikes, read json file
+ # if spikes, read json file
if os.path.isfile(params.spikes):
df = read_json(params.spikes)
spikes = []
diff --git a/workflow/rules/chipr.rules b/workflow/rules/chipr.rules
index 0bab73bfabce72588a847186a0ff3aae7fa1c546..eb0fa3ef12485e05be9748b8047202aa70b2b52d 100755
--- a/workflow/rules/chipr.rules
+++ b/workflow/rules/chipr.rules
@@ -35,8 +35,8 @@ rule chipr:
log:
out = chipr_log,
err = chipr_log_err
- #singularity:
- # "epeak.img"
+ singularity:
+ "epeak.sif"
shell:
"""
chipr -i {input} {params.opti} -o chipr_tmp > {log.out} 2> {log.err}
diff --git a/workflow/rules/computeMatrix.rules b/workflow/rules/computeMatrix.rules
index b23883a6c5c58c63334219f1b326c21de72b7611..97aa3dae4de8b6c9d3d1c3c6bb1c5b3f5b5712a9 100755
--- a/workflow/rules/computeMatrix.rules
+++ b/workflow/rules/computeMatrix.rules
@@ -34,7 +34,7 @@ rule computeMatrix:
log:
out = computeMatrix_logs
singularity:
- "epeak.img"
+ "epeak.sif"
envmodules:
"deepTools"
threads:
diff --git a/workflow/rules/compute_frip.rules b/workflow/rules/compute_frip.rules
index 20d91961a30f5b554ce84969a07337880b66ae2d..83e9aa7ea0e85104cdd2a37a7b7a27f7bab7186b 100755
--- a/workflow/rules/compute_frip.rules
+++ b/workflow/rules/compute_frip.rules
@@ -31,7 +31,7 @@ rule compute_frip:
params:
paired = compute_frip_paired
singularity:
- "epeak.img"
+ "epeak.sif"
log:
out = compute_frip_log
shell:
diff --git a/workflow/rules/compute_idr.rules b/workflow/rules/compute_idr.rules
index becc3e46e9d72de9be294e1baa1c0fdb8c517d02..b3b2b4692877aaa1da934fe04b2bd0fa2b883bd9 100755
--- a/workflow/rules/compute_idr.rules
+++ b/workflow/rules/compute_idr.rules
@@ -29,7 +29,7 @@ rule compute_idr:
idr = compute_idr_output,
peak = compute_idr_output_peak
singularity:
- "epeak.img"
+ "epeak.sif"
log:
out = compute_idr_log
params:
diff --git a/workflow/rules/cutadapt.rules b/workflow/rules/cutadapt.rules
index 4d5ee2c6be19c1673959eff61689a788e9197069..d2e433ad7212396006b2c7182ea45d0848060d48 100755
--- a/workflow/rules/cutadapt.rules
+++ b/workflow/rules/cutadapt.rules
@@ -32,10 +32,10 @@ rule cutadapt:
options = cutadapt_options,
adapters = cutadapt_adapt_list,
mode = cutadapt_mode,
- min = cutadapt_min,
- qual = cutadapt_qual
+ min = cutadapt_min,
+ qual = cutadapt_qual
singularity:
- "epeak.img"
+ "epeak.sif"
threads: config['adapters']['threads']
log:
out = cutadapt_log
diff --git a/workflow/rules/fastqc.rules b/workflow/rules/fastqc.rules
index 042d7b64e3d539f7dd44e1a22cac9d3450e47f74..0285f55341ede8b1ec9255a0fdc28958e8818aa6 100755
--- a/workflow/rules/fastqc.rules
+++ b/workflow/rules/fastqc.rules
@@ -28,7 +28,7 @@ rule fastqc:
output:
touch(fastqc_output_done)
singularity:
- "epeak.img"
+ "epeak.sif"
params:
wkdir = fastqc_wkdir,
kargs = config['fastqc']['options']
diff --git a/workflow/rules/feature_counts.rules b/workflow/rules/feature_counts.rules
index 83a23e2a9538daf2dc7672bc26d98a4ed8c52d47..912dbbbb2d3e78356149ec2ebb06de8abe9d76bc 100755
--- a/workflow/rules/feature_counts.rules
+++ b/workflow/rules/feature_counts.rules
@@ -29,7 +29,7 @@ rule feature_counts:
output:
feature_counts_output_count
singularity:
- "epeak.img"
+ "epeak.sif"
params:
mapp = feature_counts_options,
input = feature_counts_optional_input
diff --git a/workflow/rules/fragment_size_distribution.rules b/workflow/rules/fragment_size_distribution.rules
index be9a4bf3d550d944dc5311a02d5fd5835d6abb51..3940c328db75f4c43ac676a72aeca60f1841f24d 100755
--- a/workflow/rules/fragment_size_distribution.rules
+++ b/workflow/rules/fragment_size_distribution.rules
@@ -31,7 +31,7 @@ rule insert_size_metrics :
txt = insert_size_metrics_output_txt,
pdf = insert_size_metrics_histo
singularity:
- "epeak.img"
+ "epeak.sif"
log :
out = insert_size_metrics_log_out,
err = insert_size_metrics_log_err
diff --git a/workflow/rules/individualPeakAnnotation.rules b/workflow/rules/individualPeakAnnotation.rules
index 232bb713a537dde41125dc5acbf73fba06f9f424..bf4e1340c53267d7dc897923a6a833914036528b 100644
--- a/workflow/rules/individualPeakAnnotation.rules
+++ b/workflow/rules/individualPeakAnnotation.rules
@@ -23,9 +23,6 @@
rule individualPeakAnnotation:
-# RAF : inclure la librairie bx dans l'image singularity
-# singularity:
-# "epeak.img"
input:
peakAnnotation_input
@@ -34,10 +31,11 @@ rule individualPeakAnnotation:
output:
peakAnnotation_output
-
+ singularity:
+ "epeak.sif"
params:
gtf_file=config['peakAnnotation']['gtf_file'],
- standard_annotation=config['peakAnnotation']['standard'],
+ standard_annotation=config['peakAnnotation']['standard'],
gene_annotation_file=config['peakAnnotation']['gene_annotation_file'],
annotation_config=config['peakAnnotation']['config_file']
diff --git a/workflow/rules/intersectionApproach.rules b/workflow/rules/intersectionApproach.rules
index a3ecc51b72bfed51d3b87a2d120031dcc8feca5f..b7345203728f8e263efb266d26c1cb5ef9535809 100644
--- a/workflow/rules/intersectionApproach.rules
+++ b/workflow/rules/intersectionApproach.rules
@@ -30,7 +30,7 @@ rule intersectionApproach:
intersectionApproach_output
singularity:
- "epeak.img"
+ "epeak.sif"
params:
nb_min_replicates=config['intersectionApproach']['nb_min_replicates'],
diff --git a/workflow/rules/macs2.rules b/workflow/rules/macs2.rules
index 638e119f4e818b79a50ea25558e3dae8cadaa846..6be128e2548c63720c775c72c371288bba978ac7 100755
--- a/workflow/rules/macs2.rules
+++ b/workflow/rules/macs2.rules
@@ -40,7 +40,7 @@ rule macs2:
output:
macs2_output
singularity:
- "epeak.img"
+ "epeak.sif"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/macs2_noCTL.rules b/workflow/rules/macs2_noCTL.rules
index 15b2b1d7fb75b9926941dbd70bf1e051e3c1c86a..32b9ad027c9f4b15ba6d7c633ed504306d4f1f81 100755
--- a/workflow/rules/macs2_noCTL.rules
+++ b/workflow/rules/macs2_noCTL.rules
@@ -39,7 +39,7 @@ rule macs2:
output:
macs2_output
singularity:
- "epeak.img"
+ "epeak.sif"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/mark_duplicates.rules b/workflow/rules/mark_duplicates.rules
index 037be2f75c02b7ea023eaece4ccd28c4c8c5abbe..bbb1f72cafb4d17a82894aee7e31b7d0d19b23fe 100755
--- a/workflow/rules/mark_duplicates.rules
+++ b/workflow/rules/mark_duplicates.rules
@@ -30,7 +30,7 @@ rule mark_duplicates:
bam = mark_duplicates_output,
metrics = mark_duplicates_metrics
singularity:
- "epeak.img"
+ "epeak.sif"
log:
out = mark_duplicates_log_std,
err = mark_duplicates_log_err
diff --git a/workflow/rules/multiqc.rules b/workflow/rules/multiqc.rules
index ed13dd20447f3ea2d4e6eececb6927906a009884..2f2d5f513dc4fb74ab6e8bf4897708a2e300a11a 100755
--- a/workflow/rules/multiqc.rules
+++ b/workflow/rules/multiqc.rules
@@ -31,7 +31,7 @@ rule multiqc:
output:
multiqc_output
singularity:
- "epeak.img"
+ "epeak.sif"
params:
inputdir = multiqc_input_dir,
options = multiqc_options,
diff --git a/workflow/rules/plotFingerprint.rules b/workflow/rules/plotFingerprint.rules
index b2b6360def36d9a794bc4682af228ad6f70eaa40..038df6cda4d283d976d76da471fe5965f0149a86 100755
--- a/workflow/rules/plotFingerprint.rules
+++ b/workflow/rules/plotFingerprint.rules
@@ -33,7 +33,7 @@ rule plotFingerprint:
log:
out = plotFingerprint_logs
singularity:
- "epeak.img"
+ "epeak.sif"
envmodules:
"deepTools"
threads:
diff --git a/workflow/rules/plotHeatmap.rules b/workflow/rules/plotHeatmap.rules
index 2bba9676089fa4c089747604b119f7a7cce3b7c1..0cdbfa9564adac849d2577a6d8d6c0d15b7976a1 100755
--- a/workflow/rules/plotHeatmap.rules
+++ b/workflow/rules/plotHeatmap.rules
@@ -32,7 +32,7 @@ rule plotHeatmap:
log:
out = plotHeatmap_logs
singularity:
- "epeak.img"
+ "epeak.sif"
envmodules:
"deepTools"
threads:
diff --git a/workflow/rules/preIDR_PPR.rules b/workflow/rules/preIDR_PPR.rules
index 0129b9ce89766278e5675ca5b4fdd7e36d8a9fa1..2b132cfb7015eaf350f9f487cebb01471f70ca69 100755
--- a/workflow/rules/preIDR_PPR.rules
+++ b/workflow/rules/preIDR_PPR.rules
@@ -31,7 +31,7 @@ rule preIDR_PPR:
output:
preIDR_PPR_output
singularity:
- "epeak.img"
+ "epeak.sif"
shell:
"""
set -euxo pipefail
diff --git a/workflow/rules/preIDR_Pool.rules b/workflow/rules/preIDR_Pool.rules
index 64e96226ad7e0fa52799ebaf29368fcf800a34af..ad7d37d5c61088441b40d8d7152c6695ce46d048 100755
--- a/workflow/rules/preIDR_Pool.rules
+++ b/workflow/rules/preIDR_Pool.rules
@@ -31,7 +31,7 @@ rule preIDR_pool:
output:
preIDR_pool_output
singularity:
- "epeak.img"
+ "epeak.sif"
shell:
"""
set -euxo pipefail
diff --git a/workflow/rules/preIDR_SPR.rules b/workflow/rules/preIDR_SPR.rules
index 0c5b130cf8f89593e62e2bdae8424438ebe8da61..1f5a083266e6ba9461e3443a753630b33941c31b 100755
--- a/workflow/rules/preIDR_SPR.rules
+++ b/workflow/rules/preIDR_SPR.rules
@@ -31,7 +31,7 @@ rule preIDR_SPR:
output:
preIDR_SPR_output
singularity:
- "epeak.img"
+ "epeak.sif"
shell:
"""
set -euxo pipefail
diff --git a/workflow/rules/remove_biasedRegions.rules b/workflow/rules/remove_biasedRegions.rules
index 578afdbb31ca1e46fa484aa3f20917ccea5862c3..9f8ce7ad71978e56c44e07ef51b6039038576cba 100755
--- a/workflow/rules/remove_biasedRegions.rules
+++ b/workflow/rules/remove_biasedRegions.rules
@@ -28,7 +28,7 @@ rule remove_biasedRegions:
output:
bam = remove_biasedRegions_output
singularity:
- "epeak.img"
+ "epeak.sif"
log:
out = remove_biasedRegions_log_std,
err = remove_biasedRegions_log_err
diff --git a/workflow/rules/reproduciblePeakAnnotation.rules b/workflow/rules/reproduciblePeakAnnotation.rules
index 11df72516d0755e7727d8dbb85ef9df558c3f826..3973c3194d68065d8dc37b584d3becdca3f77824 100644
--- a/workflow/rules/reproduciblePeakAnnotation.rules
+++ b/workflow/rules/reproduciblePeakAnnotation.rules
@@ -23,9 +23,6 @@
rule reproduciblePeakAnnotation:
-# RAF : inclure la librairie bx dans l'image singularity
-# singularity:
-# "epeak.img"
input:
peakAnnotation_input
@@ -37,10 +34,11 @@ rule reproduciblePeakAnnotation:
params:
gtf_file=config['peakAnnotation']['gtf_file'],
- standard_annotation=config['peakAnnotation']['standard'],
+ standard_annotation=config['peakAnnotation']['standard'],
gene_annotation_file=config['peakAnnotation']['gene_annotation_file'],
annotation_config=config['peakAnnotation']['config_file']
-
+ singularity:
+ "epeak.sif"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/seacr.rules b/workflow/rules/seacr.rules
index fe61e3edceb77fc9c3e3bc25f67c745a47b184a8..a747342b400efe6ef0bbf0bbb25734d3b7007f56 100755
--- a/workflow/rules/seacr.rules
+++ b/workflow/rules/seacr.rules
@@ -34,7 +34,7 @@ rule seacr:
threshold = seacr_bed_threshold,
norm = seacr_bed_norm
singularity:
- "epeak.img"
+ "epeak.sif"
log:
out = seacr_logs_std,
err = seacr_logs_err
diff --git a/workflow/rules/seacr_noCTL.rules b/workflow/rules/seacr_noCTL.rules
index e1c75af2d199444c106b36a2db2d72b94e00ab6a..e7c73c63b542886468d58eecbdb38572c382da59 100755
--- a/workflow/rules/seacr_noCTL.rules
+++ b/workflow/rules/seacr_noCTL.rules
@@ -33,7 +33,7 @@ rule seacr:
threshold = seacr_bed_threshold,
norm = seacr_bed_norm
singularity:
- "epeak.img"
+ "epeak.sif"
log:
out = seacr_logs_std,
err = seacr_logs_err
diff --git a/workflow/rules/select_peaks.rules b/workflow/rules/select_peaks.rules
index 2375f981aebb9dbbade7eed460efa69f6ff16d2f..c2a97661425a4de0cab8647b093dcb7867c74d93 100755
--- a/workflow/rules/select_peaks.rules
+++ b/workflow/rules/select_peaks.rules
@@ -33,7 +33,7 @@ rule select_peaks:
output:
select_peaks_output
singularity:
- "epeak.img"
+ "epeak.sif"
shell:
"""
set +o pipefail
diff --git a/workflow/rules/spp.rules b/workflow/rules/spp.rules
index 1ad9d1480d5959b0eb1a9fdaf4e89262983982ce..bf3d1c16a7d4f807292f4fcbdd1017dcae564f47 100755
--- a/workflow/rules/spp.rules
+++ b/workflow/rules/spp.rules
@@ -31,7 +31,7 @@ rule spp:
params:
tmpdir = spp_tmpdir
singularity:
- "epeak.img"
+ "epeak.sif"
log:
out = spp_log_std,
err = spp_log_err
diff --git a/workflow/rules/union_peaks.rules b/workflow/rules/union_peaks.rules
index d6a755ffe854c11af000e798471cbbe42dac2bb3..25b74b3f7951924a093d4d680a6fc5c0d245867f 100755
--- a/workflow/rules/union_peaks.rules
+++ b/workflow/rules/union_peaks.rules
@@ -29,7 +29,7 @@ rule union_peaks:
output:
union_peaks_output
singularity:
- "epeak.img"
+ "epeak.sif"
shell:
"""
diff --git a/workflow/rules_atac/chipflowr_annotation.rules b/workflow/rules_atac/chipflowr_annotation.rules
index 84b2fc199449498ed14c90c570b52a14ddc3bb4b..b0d4cf835428a9797ec9662c0338de839114a552 100755
--- a/workflow/rules_atac/chipflowr_annotation.rules
+++ b/workflow/rules_atac/chipflowr_annotation.rules
@@ -24,16 +24,16 @@
rule chipflowr_annotation:
input:
- diffannot_input_dir
- log:
- diffannot_logs
+ diffannot_input_dir
output:
directory(diffannot_output_dir)
params:
gtf_file=config['peakAnnotation']['gtf_file'],
- standard_annotation=config['peakAnnotation']['standard'],
+ standard_annotation=config['peakAnnotation']['standard'],
gene_annotation_file=config['peakAnnotation']['gene_annotation_file'],
annotation_config=config['peakAnnotation']['config_file']
+ log:
+ diffannot_logs
singularity:
"epeak.sif"
shell:
diff --git a/workflow/rules_atac/chipflowr_init.rules b/workflow/rules_atac/chipflowr_init.rules
index a8954a992c947881e9d00ffd83213667a4b03052..c3d14c0d5611480edc0aa06381b40fb7b8e9fadc 100755
--- a/workflow/rules_atac/chipflowr_init.rules
+++ b/workflow/rules_atac/chipflowr_init.rules
@@ -49,9 +49,9 @@ rule chipflowr_init:
cwd = os.getcwd()
# Sed on matrix to get MARK_COND_REP as sample names
if 'NobiasedRegions' in open(input.matrix).read():
- shell("sed -i -E 's/((\/[A-Za-z0-9._-]+){{0,}})(\/04-NobiasedRegions\/)//g' %s && sed -i 's/_%s_sort_dedup_biasedRegions.bam//g' %s" % (input.matrix, params.genome, input.matrix))
+ shell("sed -i -E 's/((\/?[A-Za-z0-9._-]+){{0,}})(\/04-NobiasedRegions\/)//g' %s && sed -i 's/_%s_sort_dedup_biasedRegions.bam//g' %s" % (input.matrix, params.genome, input.matrix))
elif 'Deduplication' in open(input.matrix).read():
- shell("sed -i -E 's/((\/[A-Za-z0-9._-]+){{0,}})(\/03-Deduplication\/)//g' %s && sed -i 's/_%s_sort_dedup.bam//g' %s " % (input.matrix, params.genome, input.matrix))
+ shell("sed -i -E 's/((\/?[A-Za-z0-9._-]+){{0,}})(\/03-Deduplication\/)//g' %s && sed -i 's/_%s_sort_dedup.bam//g' %s " % (input.matrix, params.genome, input.matrix))
# get cond and rep vectors
samples = (linecache.getline(input.matrix, 2)).rstrip().split('\t')[6:]
diff --git a/workflow/rules_atac/cutadapt.rules b/workflow/rules_atac/cutadapt.rules
index cb94a8574a48600c432ce71fd8ba388a702d0339..7400f1ebd6233c94cc8f11345edca203915ab2f3 100755
--- a/workflow/rules_atac/cutadapt.rules
+++ b/workflow/rules_atac/cutadapt.rules
@@ -33,7 +33,7 @@ rule cutadapt:
adapters = cutadapt_adapt_list,
mode = cutadapt_mode,
min = cutadapt_min,
- qual = cutadapt_qual,
+ qual = cutadapt_qual
singularity:
"epeak.sif"
threads: config['adapters']['threads']
diff --git a/workflow/rules_atac/individualPeakAnnotation.rules b/workflow/rules_atac/individualPeakAnnotation.rules
index 201ddadd290459276b8ce1292050f3bea57517b2..a5c08d732e4433e87f5a436c6de11a658de08078 100755
--- a/workflow/rules_atac/individualPeakAnnotation.rules
+++ b/workflow/rules_atac/individualPeakAnnotation.rules
@@ -23,8 +23,6 @@
rule individualPeakAnnotation:
- singularity:
- "epeak.sif"
input:
peakAnnotation_input
log:
@@ -33,9 +31,11 @@ rule individualPeakAnnotation:
peakAnnotation_output
params:
gtf_file=config['peakAnnotation']['gtf_file'],
- standard_annotation=config['peakAnnotation']['standard'],
+ standard_annotation=config['peakAnnotation']['standard'],
gene_annotation_file=config['peakAnnotation']['gene_annotation_file'],
annotation_config=config['peakAnnotation']['config_file']
+ singularity:
+ "epeak.sif"
shell:
"""
set +o pipefail
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