['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=60000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:34:08 2024] rule rule_7_peaks_annotation: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_peaks_filtered.narrowPeak, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_peaks_filtered.narrowPeak output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/7_peaks_annotation/report_annotation_homer.txt log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/7_check_peaks.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/7_intersect_bed.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/7_peaks_annotation_cut.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/7_peaks_annotation_peaks.txt jobid: 0 reason: Forced execution resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=60000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bedtools multiinter -i /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_peaks_filtered.narrowPeak /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_peaks_filtered.narrowPeak -header Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1.bed Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2.bed > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/7_peaks_annotation/report_multi_intersectBed.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/7_intersect_bed.txt; cut -f1-3 /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/7_peaks_annotation/report_multi_intersectBed.txt > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/7_peaks_annotation/report.bed 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/7_peaks_annotation_cut.txt; export PATH=$PATH:/opt/miniconda3/envs/utap/bin; annotatePeaks.pl /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/7_peaks_annotation/report.bed /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa -gtf /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/7_peaks_annotation/report_annotation_homer.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/7_peaks_annotation_peaks.txt [Tue Nov 19 05:34:44 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=8989, disk_mb=8989, mem_mb_per_thread=60000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:25:37 2024] rule rule_6_peaks_prediction_with_control: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_sorted.bam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_sorted.bam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_sorted.bam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_sorted.bam output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_peaks.narrowPeak, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_model.r, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_peaks_filtered.narrowPeak log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/6_peaks_prediction_Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1.txt jobid: 0 reason: Forced execution wildcards: treat=Runx3_CD4DC_IP1, control=Runx3_CD4DC_input1 resources: mem_mb=8989, disk_mb=8989, tmpdir=/tmp, mem_mb_per_thread=60000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_sorted.bam -c /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_sorted.bam --bw 300 -B -f BAM --SPMR -g mm -n Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1 --keep-dup auto -q 0.05 --outdir /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction &>/home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/6_peaks_prediction_Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1.txt & wait cd /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction && /opt/miniconda3/envs/utap/bin/R --vanilla --slave < /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_model.r >> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/6_peaks_prediction_Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1.txt /opt/miniconda3/envs/utap/bin/bedtools intersect -a /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_peaks.narrowPeak -b /shareDB/genomes/Mus_musculus/UCSC/mm10/Black_list/mm10-blacklist.v2.bed -v | /opt/miniconda3/envs/utap/bin/bedtools sort -i - > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_peaks_filtered.narrowPeak 2>> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/6_peaks_prediction_Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1.txt [Tue Nov 19 05:29:33 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=14793, disk_mb=14793, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:11:37 2024] rule rule_5_filtered_alignment: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP1.sam output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_rm_not_uniq.sam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_sorted.bam log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP1_rm_not_uniq.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP1.sort.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP1.index.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP1.flagstat.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_IP1 threads: 5 resources: mem_mb=14793, disk_mb=14793, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 /opt/miniconda3/envs/utap/bin/samtools view -h -q 39 -F 4 /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP1.sam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_rm_not_uniq.sam 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP1_rm_not_uniq.txt /opt/miniconda3/envs/utap/bin/samtools view -SB -h /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_rm_not_uniq.sam | /opt/miniconda3/envs/utap/bin/samtools sort -T /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_sorted.bam - > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP1.sort.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_sorted.bam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP1.index.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_sorted.bam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_flagstat.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP1.flagstat.txt touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_rm_not_uniq.sam.deleted [Tue Nov 19 05:14:14 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3267, disk_mb=3267, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:07:05 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP1.sam log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/4_mapping.Runx3_CD4DC_IP1.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_IP1 threads: 20 resources: mem_mb=3267, disk_mb=3267, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie2 -p 20 -x /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 -U /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1.fastq.gz -S /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP1.sam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP1.stat 2>&1; touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP1.sam.deleted touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP1.sam.deleted [Tue Nov 19 05:11:16 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=16003, disk_mb=16003, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:19:44 2024] rule rule_5_filtered_alignment: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input2.sam output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_rm_not_uniq.sam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_sorted.bam log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input2_rm_not_uniq.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input2.sort.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input2.index.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input2.flagstat.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_input2 threads: 5 resources: mem_mb=16003, disk_mb=16003, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 /opt/miniconda3/envs/utap/bin/samtools view -h -q 39 -F 4 /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input2.sam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_rm_not_uniq.sam 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input2_rm_not_uniq.txt /opt/miniconda3/envs/utap/bin/samtools view -SB -h /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_rm_not_uniq.sam | /opt/miniconda3/envs/utap/bin/samtools sort -T /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_sorted.bam - > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input2.sort.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_sorted.bam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input2.index.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_sorted.bam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_flagstat.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input2.flagstat.txt touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_rm_not_uniq.sam.deleted [Tue Nov 19 05:22:34 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3521, disk_mb=3521, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:15:00 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input2.sam log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/4_mapping.Runx3_CD4DC_input2.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_input2 threads: 20 resources: mem_mb=3521, disk_mb=3521, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie2 -p 20 -x /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 -U /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1.fastq.gz -S /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input2.sam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input2.stat 2>&1; touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input2.sam.deleted touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input2.sam.deleted [Tue Nov 19 05:19:29 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=12713, disk_mb=12713, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:15:06 2024] rule rule_5_filtered_alignment: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP2.sam output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_rm_not_uniq.sam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_sorted.bam log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP2_rm_not_uniq.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP2.sort.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP2.index.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP2.flagstat.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_IP2 threads: 5 resources: mem_mb=12713, disk_mb=12713, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 /opt/miniconda3/envs/utap/bin/samtools view -h -q 39 -F 4 /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP2.sam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_rm_not_uniq.sam 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP2_rm_not_uniq.txt /opt/miniconda3/envs/utap/bin/samtools view -SB -h /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_rm_not_uniq.sam | /opt/miniconda3/envs/utap/bin/samtools sort -T /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_sorted.bam - > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP2.sort.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_sorted.bam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP2.index.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_sorted.bam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_flagstat.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_IP2.flagstat.txt touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_rm_not_uniq.sam.deleted [Tue Nov 19 05:17:17 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2816, disk_mb=2816, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:11:20 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP2.sam log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/4_mapping.Runx3_CD4DC_IP2.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_IP2 threads: 20 resources: mem_mb=2816, disk_mb=2816, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie2 -p 20 -x /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 -U /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1.fastq.gz -S /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP2.sam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP2.stat 2>&1; touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP2.sam.deleted touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_IP2.sam.deleted [Tue Nov 19 05:14:55 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=13465, disk_mb=13465, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:20:50 2024] rule rule_5_filtered_alignment: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input1.sam output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_rm_not_uniq.sam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_sorted.bam log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input1_rm_not_uniq.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input1.sort.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input1.index.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input1.flagstat.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_input1 threads: 5 resources: mem_mb=13465, disk_mb=13465, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 /opt/miniconda3/envs/utap/bin/samtools view -h -q 39 -F 4 /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input1.sam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_rm_not_uniq.sam 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input1_rm_not_uniq.txt /opt/miniconda3/envs/utap/bin/samtools view -SB -h /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_rm_not_uniq.sam | /opt/miniconda3/envs/utap/bin/samtools sort -T /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_sorted.bam - > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input1.sort.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_sorted.bam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input1.index.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_sorted.bam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_flagstat.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/5_filtered_alignment.Runx3_CD4DC_input1.flagstat.txt touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_rm_not_uniq.sam.deleted [Tue Nov 19 05:25:23 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=20000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:21:11 2024] rule rule_3_multiQC: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1_fastqc/fastqc_data.txt output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/3_multiQC/multiqc_report.html log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/3_multiQC.txt jobid: 0 reason: Forced execution resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=20000, mem_mb_total=20000 /opt/miniconda3/envs/utap/bin/multiqc -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/3_multiQC /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc &>/home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/3_multiQC.txt [Tue Nov 19 05:21:18 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2936, disk_mb=2936, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:17:03 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input1.sam log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/4_mapping.Runx3_CD4DC_input1.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_input1 threads: 20 resources: mem_mb=2936, disk_mb=2936, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie2 -p 20 -x /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 -U /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1.fastq.gz -S /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input1.sam > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input1.stat 2>&1; touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input1.sam.deleted touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/4_mapping/Runx3_CD4DC_input1.sam.deleted [Tue Nov 19 05:20:30 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=8989, disk_mb=8989, mem_mb_per_thread=60000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:25:43 2024] rule rule_6_peaks_prediction_with_control: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_sorted.bam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_sorted.bam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_sorted.bam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_sorted.bam output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_peaks.narrowPeak, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_model.r, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_peaks_filtered.narrowPeak log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/6_peaks_prediction_Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2.txt jobid: 0 reason: Forced execution wildcards: treat=Runx3_CD4DC_IP2, control=Runx3_CD4DC_input2 resources: mem_mb=8989, disk_mb=8989, tmpdir=/tmp, mem_mb_per_thread=60000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_sorted.bam -c /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_sorted.bam --bw 300 -B -f BAM --SPMR -g mm -n Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2 --keep-dup auto -q 0.05 --outdir /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction &>/home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/6_peaks_prediction_Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2.txt & wait cd /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction && /opt/miniconda3/envs/utap/bin/R --vanilla --slave < /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_model.r >> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/6_peaks_prediction_Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2.txt /opt/miniconda3/envs/utap/bin/bedtools intersect -a /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_peaks.narrowPeak -b /shareDB/genomes/Mus_musculus/UCSC/mm10/Black_list/mm10-blacklist.v2.bed -v | /opt/miniconda3/envs/utap/bin/bedtools sort -i - > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_peaks_filtered.narrowPeak 2>> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/6_peaks_prediction_Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2.txt [Tue Nov 19 05:33:52 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=8989, disk_mb=8989, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:38:03 2024] rule rule_8_graphs: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP1_sorted.bam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input2_sorted.bam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_IP2_sorted.bam, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/5_filtered_alignment/Runx3_CD4DC_input1_sorted.bam output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/8_graphs/samples.avgprof.pdf log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/8_graphs.txt jobid: 0 reason: Forced execution threads: 20 resources: mem_mb=8989, disk_mb=8989, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 [Tue Nov 19 05:40:44 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=9484, disk_mb=9484, mem_mb_per_thread=60000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:34:06 2024] rule rule_9_bdg2BigWig: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/9_BigWig/Runx3_CD4DC_IP1_treat_pileup.bw, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/9_BigWig/Runx3_CD4DC_IP2_treat_pileup.bw, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/9_BigWig/Runx3_CD4DC_input2_control_lambda.bw, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/9_BigWig/Runx3_CD4DC_input1_control_lambda.bw log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_slop.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_sort.txt, /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_bed2bigwig.txt jobid: 0 reason: Forced execution resources: mem_mb=9484, disk_mb=9484, tmpdir=/tmp, mem_mb_per_thread=60000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bedtools slop -i /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg -g /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes -b 0 | /opt/miniconda3/envs/utap/bin/bedClip stdin /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg.clip > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_slop.txt 2>&1; LC_COLLATE=C; sort -k1,1 -k2,2n /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg.clip > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg.sort.clip 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_sort.txt; /opt/miniconda3/envs/utap/bin/bedGraphToBigWig /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg.sort.clip /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/9_BigWig/Runx3_CD4DC_IP1_treat_pileup.bw > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_bed2bigwig.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg.clip.deleted /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg.sort.clip.deleted; rm -f /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg.clip /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_treat_pileup.bdg.sort.clip; /opt/miniconda3/envs/utap/bin/bedtools slop -i /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg -g /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes -b 0 | /opt/miniconda3/envs/utap/bin/bedClip stdin /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg.clip > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_slop.txt 2>&1; LC_COLLATE=C; sort -k1,1 -k2,2n /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg.clip > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg.sort.clip 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_sort.txt; /opt/miniconda3/envs/utap/bin/bedGraphToBigWig /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg.sort.clip /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/9_BigWig/Runx3_CD4DC_IP2_treat_pileup.bw > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_bed2bigwig.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg.clip.deleted /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg.sort.clip.deleted; rm -f /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg.clip /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_treat_pileup.bdg.sort.clip; /opt/miniconda3/envs/utap/bin/bedtools slop -i /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg -g /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes -b 0 | /opt/miniconda3/envs/utap/bin/bedClip stdin /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg.clip > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_slop.txt 2>&1; LC_COLLATE=C; sort -k1,1 -k2,2n /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg.clip > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg.sort.clip 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_sort.txt; /opt/miniconda3/envs/utap/bin/bedGraphToBigWig /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg.sort.clip /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/9_BigWig/Runx3_CD4DC_input1_control_lambda.bw > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_bed2bigwig.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg.clip.deleted /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg.sort.clip.deleted; rm -f /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg.clip /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP1_vs_Runx3_CD4DC_input1_control_lambda.bdg.sort.clip; /opt/miniconda3/envs/utap/bin/bedtools slop -i /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg -g /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes -b 0 | /opt/miniconda3/envs/utap/bin/bedClip stdin /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg.clip > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_slop.txt 2>&1; LC_COLLATE=C; sort -k1,1 -k2,2n /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg.clip > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg.sort.clip 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_sort.txt; /opt/miniconda3/envs/utap/bin/bedGraphToBigWig /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg.sort.clip /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/9_BigWig/Runx3_CD4DC_input2_control_lambda.bw > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/9_BigWig_bed2bigwig.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg.clip.deleted /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg.sort.clip.deleted; rm -f /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg.clip /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/6_peaks_prediction/Runx3_CD4DC_IP2_vs_Runx3_CD4DC_input2_control_lambda.bdg.sort.clip; [Tue Nov 19 05:44:21 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3267, disk_mb=3267, mem_mb_per_thread=200, mem_mb_total=1000 Select jobs to execute... [Tue Nov 19 05:16:48 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/2_fastqc.Runx3_CD4DC_IP1.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_IP1 threads: 5 resources: mem_mb=3267, disk_mb=3267, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=1000 mkdir -p /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_IP1 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_IP1 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/2_fastqc.Runx3_CD4DC_IP1.txt 2>&1 [Tue Nov 19 05:18:45 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=17357, disk_mb=17357, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:49:39 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/Dicken_fastq/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1.fastq output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/1_cutadapt.Runx3_CD4DC_IP1.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_IP1 threads: 4 resources: mem_mb=17357, disk_mb=17357, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/Dicken_fastq/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1.fastq > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/1_cutadapt.Runx3_CD4DC_IP1.txt touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP1/Runx3_CD4DC_IP1_R1.fastq.gz.deleted [Tue Nov 19 04:51:23 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3521, disk_mb=3521, mem_mb_per_thread=200, mem_mb_total=1000 Select jobs to execute... [Tue Nov 19 05:14:29 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/2_fastqc.Runx3_CD4DC_input2.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_input2 threads: 5 resources: mem_mb=3521, disk_mb=3521, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=1000 mkdir -p /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_input2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_input2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/2_fastqc.Runx3_CD4DC_input2.txt 2>&1 [Tue Nov 19 05:16:27 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=18608, disk_mb=18608, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:49:41 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/Dicken_fastq/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1.fastq output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/1_cutadapt.Runx3_CD4DC_input2.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_input2 threads: 4 resources: mem_mb=18608, disk_mb=18608, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/Dicken_fastq/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1.fastq > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/1_cutadapt.Runx3_CD4DC_input2.txt touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input2/Runx3_CD4DC_input2_R1.fastq.gz.deleted [Tue Nov 19 04:51:27 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2816, disk_mb=2816, mem_mb_per_thread=200, mem_mb_total=1000 Select jobs to execute... [Tue Nov 19 05:19:07 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/2_fastqc.Runx3_CD4DC_IP2.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_IP2 threads: 5 resources: mem_mb=2816, disk_mb=2816, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=1000 mkdir -p /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_IP2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_IP2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/2_fastqc.Runx3_CD4DC_IP2.txt 2>&1 [Tue Nov 19 05:20:42 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=14770, disk_mb=14770, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:49:41 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/Dicken_fastq/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1.fastq output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/1_cutadapt.Runx3_CD4DC_IP2.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_IP2 threads: 4 resources: mem_mb=14770, disk_mb=14770, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/Dicken_fastq/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1.fastq > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/1_cutadapt.Runx3_CD4DC_IP2.txt touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_IP2/Runx3_CD4DC_IP2_R1.fastq.gz.deleted [Tue Nov 19 04:51:08 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2936, disk_mb=2936, mem_mb_per_thread=200, mem_mb_total=1000 Select jobs to execute... [Tue Nov 19 05:17:37 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/2_fastqc.Runx3_CD4DC_input1.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_input1 threads: 5 resources: mem_mb=2936, disk_mb=2936, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=1000 mkdir -p /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_input1 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/2_fastqc/Runx3_CD4DC_input1 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/2_fastqc.Runx3_CD4DC_input1.txt 2>&1 [Tue Nov 19 05:19:46 2024] Finished job 0. 1 of 1 steps (100%) done ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_input2', 'Runx3_CD4DC_IP2', 'Runx3_CD4DC_input1'] {} ['Runx3_CD4DC_IP1', 'Runx3_CD4DC_IP2'] ['Runx3_CD4DC_input1', 'Runx3_CD4DC_input2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=15648, disk_mb=15648, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:49:41 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/Dicken_fastq/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1.fastq output: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/1_cutadapt.Runx3_CD4DC_input1.txt jobid: 0 reason: Forced execution wildcards: sample=Runx3_CD4DC_input1 threads: 4 resources: mem_mb=15648, disk_mb=15648, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/Dicken_fastq/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1.fastq > /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/logs_20241119_044920/1_cutadapt.Runx3_CD4DC_input1.txt touch /home/labs/bioservices/Collaboration/example_ChIP_Dicken_DC_Runx/20241119_044920_data_for_demo_production_ChIP-Seq/1_cutadapt/Runx3_CD4DC_input1/Runx3_CD4DC_input1_R1.fastq.gz.deleted [Tue Nov 19 04:51:33 2024] Finished job 0. 1 of 1 steps (100%) done