['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:28:48 2024] rule rule_7_shift_bam: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free_shift.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_bam2bed.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_shift_bam.Aire_C313Y_WT2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT2 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 /opt/miniconda3/envs/utap/bin/bedtools bamtobed -i /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_bam2bed.Aire_C313Y_WT2.txt && cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free.bed | awk -F $' ' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' >| /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free_shift.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_shift_bam.Aire_C313Y_WT2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free.bed.deleted [Tue Nov 19 05:29:05 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=1731, disk_mb=1731, mem_mb_per_thread=100, mem_mb_total=100 Select jobs to execute... [Tue Nov 19 05:27:39 2024] rule rule_6_nucleosome_free: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.sam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.statistics log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_header.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_sam2bam.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_index.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_statistics.Aire_C313Y_WT2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT2 resources: mem_mb=1731, disk_mb=1731, tmpdir=/tmp, mem_mb_per_thread=100, mem_mb_total=100 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.sam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_header.Aire_C313Y_WT2.txt /opt/miniconda3/envs/utap/bin/samtools view /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam | awk -F " " '{if (($9 > -120) && ($9 < 120)) print $_}' >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.sam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free.Aire_C313Y_WT2.txt /opt/miniconda3/envs/utap/bin/samtools view -h -b /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_sam2bam.Aire_C313Y_WT2.txt /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_index.Aire_C313Y_WT2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.statistics 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_statistics.Aire_C313Y_WT2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.sam.deleted [Tue Nov 19 05:28:35 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=34549, disk_mb=34549, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:07:14 2024] rule rule_5_process_alignment: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT2.sam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_mito.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_not_uniq.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_sorted.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito_stat.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq_stat.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_sort.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_index.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup_stat.Aire_C313Y_WT2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT2 threads: 5 resources: mem_mb=34549, disk_mb=34549, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 grep -v 'chrM' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT2.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_mito.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito.Aire_C313Y_WT2.txt /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_mito.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_mito_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito_stat.Aire_C313Y_WT2.txt /opt/miniconda3/envs/utap/bin/samtools view -q 39 -b -h -F 4 -f 0x2 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_mito.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_not_uniq.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq.Aire_C313Y_WT2.txt /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_not_uniq.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_not_uniq_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq_stat.Aire_C313Y_WT2.txt /opt/miniconda3/envs/utap/bin/picard SortSam SO=coordinate I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_not_uniq.bam O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_sorted.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_sort.Aire_C313Y_WT2.txt 2>&1 /opt/miniconda3/envs/utap/bin/picard MarkDuplicates INPUT=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_sorted.bam OUTPUT=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam M=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup_metrics.txt REMOVE_DUPLICATES=true > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup.Aire_C313Y_WT2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_index.Aire_C313Y_WT2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup_stat.Aire_C313Y_WT2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_mito.bam.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_not_uniq.bam.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_sorted.bam.deleted [Tue Nov 19 05:23:26 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=4376, disk_mb=4376, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 04:50:53 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT2.sam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/4_mapping.Aire_C313Y_WT2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT2 threads: 20 resources: mem_mb=4376, disk_mb=4376, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie2 -X 2000 --local -p 20 -x /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 -1 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R1.fastq.gz -2 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R2.fastq.gz -S /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT2.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT2.stat 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT2.sam.deleted [Tue Nov 19 05:07:02 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=4925, disk_mb=4925, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:47:48 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_WT2/Aire_C313Y_WT2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_WT2/Aire_C313Y_WT2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R2.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/1_cutadapt.Aire_C313Y_WT2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT2 threads: 4 resources: mem_mb=4925, disk_mb=4925, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 #Running in parallel is not supported on Python 2 /opt/miniconda3/envs/utap/bin/cutadapt -q 25 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGAGTGTAGATCTCGGTGGTCGCCGTATCATT --minimum-length 30 -j 4 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R1.fastq.gz -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R2.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_WT2/Aire_C313Y_WT2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_WT2/Aire_C313Y_WT2_R2.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/1_cutadapt.Aire_C313Y_WT2.txt; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R1.fastq.gz.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R2.fastq.gz.deleted [Tue Nov 19 04:50:39 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=3000, mem_mb_total=3000 Select jobs to execute... [Tue Nov 19 05:41:44 2024] rule rule_11_call_peak_without_control: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free_shift.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het3_peaks.broadPeak/Aire_C313Y_Het3_peaks.broadPeak, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het3_peaks.broadPeak/Aire_C313Y_Het3_peaks_filtered.broadPeak log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_Het3.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het3 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=3000 /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free_shift.bed --bw 120 -B -f BEDPE --SPMR -B -g mm --nomodel -n Aire_C313Y_Het3 --shift -50 --extsize 100 --broad --keep-dup all -q 0.05 --outdir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het3_peaks.broadPeak > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_Het3.txt 2>&1 & wait /opt/miniconda3/envs/utap/bin/bedtools intersect -a /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het3_peaks.broadPeak/Aire_C313Y_Het3_peaks.broadPeak -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_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het3_peaks.broadPeak/Aire_C313Y_Het3_peaks_filtered.broadPeak 2>> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_Het3.txt [Tue Nov 19 05:42:31 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:40:43 2024] rule rule_7_shift_bam: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free_shift.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_bam2bed.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_shift_bam.Aire_C313Y_Het3.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het3 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 /opt/miniconda3/envs/utap/bin/bedtools bamtobed -i /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_bam2bed.Aire_C313Y_Het3.txt && cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free.bed | awk -F $' ' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' >| /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free_shift.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_shift_bam.Aire_C313Y_Het3.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free.bed.deleted [Tue Nov 19 05:41:00 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=1510, disk_mb=1510, mem_mb_per_thread=100, mem_mb_total=100 Select jobs to execute... [Tue Nov 19 05:38:52 2024] rule rule_6_nucleosome_free: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.sam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.statistics log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_header.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_sam2bam.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_index.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_statistics.Aire_C313Y_Het3.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het3 resources: mem_mb=1510, disk_mb=1510, tmpdir=/tmp, mem_mb_per_thread=100, mem_mb_total=100 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.sam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_header.Aire_C313Y_Het3.txt /opt/miniconda3/envs/utap/bin/samtools view /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam | awk -F " " '{if (($9 > -120) && ($9 < 120)) print $_}' >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.sam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free.Aire_C313Y_Het3.txt /opt/miniconda3/envs/utap/bin/samtools view -h -b /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_sam2bam.Aire_C313Y_Het3.txt /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_index.Aire_C313Y_Het3.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.statistics 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_statistics.Aire_C313Y_Het3.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.sam.deleted [Tue Nov 19 05:40:31 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=29499, disk_mb=29499, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:17:14 2024] rule rule_5_process_alignment: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het3.sam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_mito.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_not_uniq.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_sorted.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito_stat.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq_stat.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_sort.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_index.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup_stat.Aire_C313Y_Het3.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het3 threads: 5 resources: mem_mb=29499, disk_mb=29499, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 grep -v 'chrM' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het3.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_mito.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito.Aire_C313Y_Het3.txt /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_mito.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_mito_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito_stat.Aire_C313Y_Het3.txt /opt/miniconda3/envs/utap/bin/samtools view -q 39 -b -h -F 4 -f 0x2 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_mito.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_not_uniq.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq.Aire_C313Y_Het3.txt /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_not_uniq.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_not_uniq_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq_stat.Aire_C313Y_Het3.txt /opt/miniconda3/envs/utap/bin/picard SortSam SO=coordinate I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_not_uniq.bam O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_sorted.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_sort.Aire_C313Y_Het3.txt 2>&1 /opt/miniconda3/envs/utap/bin/picard MarkDuplicates INPUT=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_sorted.bam OUTPUT=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam M=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup_metrics.txt REMOVE_DUPLICATES=true > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup.Aire_C313Y_Het3.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_index.Aire_C313Y_Het3.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup_stat.Aire_C313Y_Het3.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_mito.bam.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_not_uniq.bam.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_sorted.bam.deleted [Tue Nov 19 05:38:23 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3780, disk_mb=3780, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:04:01 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het3.sam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/4_mapping.Aire_C313Y_Het3.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het3 threads: 20 resources: mem_mb=3780, disk_mb=3780, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie2 -X 2000 --local -p 20 -x /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 -1 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R1.fastq.gz -2 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R2.fastq.gz -S /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het3.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het3.stat 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het3.sam.deleted [Tue Nov 19 05:16:58 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=4263, disk_mb=4263, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:47:48 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_Het3/Aire_C313Y_Het3_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_Het3/Aire_C313Y_Het3_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R2.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/1_cutadapt.Aire_C313Y_Het3.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het3 threads: 4 resources: mem_mb=4263, disk_mb=4263, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 #Running in parallel is not supported on Python 2 /opt/miniconda3/envs/utap/bin/cutadapt -q 25 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGAGTGTAGATCTCGGTGGTCGCCGTATCATT --minimum-length 30 -j 4 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R1.fastq.gz -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R2.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_Het3/Aire_C313Y_Het3_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_Het3/Aire_C313Y_Het3_R2.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/1_cutadapt.Aire_C313Y_Het3.txt; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R1.fastq.gz.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R2.fastq.gz.deleted [Tue Nov 19 04:50:39 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=3000, mem_mb_total=3000 Select jobs to execute... [Tue Nov 19 05:32:39 2024] rule rule_11_call_peak_without_control: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free_shift.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het2_peaks.broadPeak/Aire_C313Y_Het2_peaks.broadPeak, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het2_peaks.broadPeak/Aire_C313Y_Het2_peaks_filtered.broadPeak log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_Het2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=3000 /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free_shift.bed --bw 120 -B -f BEDPE --SPMR -B -g mm --nomodel -n Aire_C313Y_Het2 --shift -50 --extsize 100 --broad --keep-dup all -q 0.05 --outdir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het2_peaks.broadPeak > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_Het2.txt 2>&1 & wait /opt/miniconda3/envs/utap/bin/bedtools intersect -a /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het2_peaks.broadPeak/Aire_C313Y_Het2_peaks.broadPeak -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_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het2_peaks.broadPeak/Aire_C313Y_Het2_peaks_filtered.broadPeak 2>> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_Het2.txt [Tue Nov 19 05:33:38 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:28:25 2024] rule rule_7_shift_bam: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free_shift.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_bam2bed.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_shift_bam.Aire_C313Y_Het2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het2 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 /opt/miniconda3/envs/utap/bin/bedtools bamtobed -i /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_bam2bed.Aire_C313Y_Het2.txt && cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free.bed | awk -F $' ' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' >| /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free_shift.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_shift_bam.Aire_C313Y_Het2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free.bed.deleted [Tue Nov 19 05:28:45 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=1651, disk_mb=1651, mem_mb_per_thread=100, mem_mb_total=100 Select jobs to execute... [Tue Nov 19 05:26:11 2024] rule rule_6_nucleosome_free: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.sam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.statistics log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_header.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_sam2bam.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_index.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_statistics.Aire_C313Y_Het2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het2 resources: mem_mb=1651, disk_mb=1651, tmpdir=/tmp, mem_mb_per_thread=100, mem_mb_total=100 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.sam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_header.Aire_C313Y_Het2.txt /opt/miniconda3/envs/utap/bin/samtools view /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam | awk -F " " '{if (($9 > -120) && ($9 < 120)) print $_}' >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.sam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free.Aire_C313Y_Het2.txt /opt/miniconda3/envs/utap/bin/samtools view -h -b /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_sam2bam.Aire_C313Y_Het2.txt /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_index.Aire_C313Y_Het2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.statistics 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_statistics.Aire_C313Y_Het2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.sam.deleted [Tue Nov 19 05:28:12 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=31294, disk_mb=31294, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:04:14 2024] rule rule_5_process_alignment: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het2.sam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_mito.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_not_uniq.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_sorted.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito_stat.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq_stat.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_sort.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_index.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup_stat.Aire_C313Y_Het2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het2 threads: 5 resources: mem_mb=31294, disk_mb=31294, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 grep -v 'chrM' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het2.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_mito.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito.Aire_C313Y_Het2.txt /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_mito.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_mito_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito_stat.Aire_C313Y_Het2.txt /opt/miniconda3/envs/utap/bin/samtools view -q 39 -b -h -F 4 -f 0x2 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_mito.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_not_uniq.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq.Aire_C313Y_Het2.txt /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_not_uniq.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_not_uniq_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq_stat.Aire_C313Y_Het2.txt /opt/miniconda3/envs/utap/bin/picard SortSam SO=coordinate I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_not_uniq.bam O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_sorted.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_sort.Aire_C313Y_Het2.txt 2>&1 /opt/miniconda3/envs/utap/bin/picard MarkDuplicates INPUT=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_sorted.bam OUTPUT=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam M=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup_metrics.txt REMOVE_DUPLICATES=true > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup.Aire_C313Y_Het2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_index.Aire_C313Y_Het2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup_stat.Aire_C313Y_Het2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_mito.bam.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_not_uniq.bam.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_sorted.bam.deleted [Tue Nov 19 05:21:14 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=4034, disk_mb=4034, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 04:51:34 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het2.sam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/4_mapping.Aire_C313Y_Het2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het2 threads: 20 resources: mem_mb=4034, disk_mb=4034, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie2 -X 2000 --local -p 20 -x /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 -1 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R1.fastq.gz -2 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R2.fastq.gz -S /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het2.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het2.stat 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_Het2.sam.deleted [Tue Nov 19 05:03:55 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=4550, disk_mb=4550, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:47:52 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_Het2/Aire_C313Y_Het2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_Het2/Aire_C313Y_Het2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R2.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/1_cutadapt.Aire_C313Y_Het2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het2 threads: 4 resources: mem_mb=4550, disk_mb=4550, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 #Running in parallel is not supported on Python 2 /opt/miniconda3/envs/utap/bin/cutadapt -q 25 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGAGTGTAGATCTCGGTGGTCGCCGTATCATT --minimum-length 30 -j 4 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R1.fastq.gz -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R2.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_Het2/Aire_C313Y_Het2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_Het2/Aire_C313Y_Het2_R2.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/1_cutadapt.Aire_C313Y_Het2.txt; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R1.fastq.gz.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R2.fastq.gz.deleted [Tue Nov 19 04:50:40 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5468, disk_mb=5468, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:21:29 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_WT1/Aire_C313Y_WT1_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/2_fastqc.Aire_C313Y_WT1.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT1 threads: 5 resources: mem_mb=5468, disk_mb=5468, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_WT1 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_WT1 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R2.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/2_fastqc.Aire_C313Y_WT1.txt 2>&1 [Tue Nov 19 05:23:54 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=4376, disk_mb=4376, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:23:48 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_WT2/Aire_C313Y_WT2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/2_fastqc.Aire_C313Y_WT2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT2 threads: 5 resources: mem_mb=4376, disk_mb=4376, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_WT2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_WT2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT2/Aire_C313Y_WT2_R2.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/2_fastqc.Aire_C313Y_WT2.txt 2>&1 [Tue Nov 19 05:25:25 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3780, disk_mb=3780, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:25:32 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_Het3/Aire_C313Y_Het3_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/2_fastqc.Aire_C313Y_Het3.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het3 threads: 5 resources: mem_mb=3780, disk_mb=3780, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_Het3 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_Het3 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het3/Aire_C313Y_Het3_R2.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/2_fastqc.Aire_C313Y_Het3.txt 2>&1 [Tue Nov 19 05:27:19 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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 05:59:57 2024] rule rule_12_peaks_annotation: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT1_peaks.broadPeak/Aire_C313Y_WT1_peaks_filtered.broadPeak, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT2_peaks.broadPeak/Aire_C313Y_WT2_peaks_filtered.broadPeak, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het3_peaks.broadPeak/Aire_C313Y_Het3_peaks_filtered.broadPeak, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het2_peaks.broadPeak/Aire_C313Y_Het2_peaks_filtered.broadPeak output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/12_peaks_annotation/report_annotation_homer.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/12_check_peaks.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/12_intersect_bed.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/12_peaks_annotation_cut.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/12_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_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT1_peaks.broadPeak/Aire_C313Y_WT1_peaks_filtered.broadPeak /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT2_peaks.broadPeak/Aire_C313Y_WT2_peaks_filtered.broadPeak /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het3_peaks.broadPeak/Aire_C313Y_Het3_peaks_filtered.broadPeak /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_Het2_peaks.broadPeak/Aire_C313Y_Het2_peaks_filtered.broadPeak -header Aire_C313Y_WT1.bed Aire_C313Y_WT2.bed Aire_C313Y_Het3.bed Aire_C313Y_Het2.bed > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/12_peaks_annotation/report_multi_intersectBed.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/12_intersect_bed.txt; cut -f1-3 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/12_peaks_annotation/report_multi_intersectBed.txt > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/12_peaks_annotation/report.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/12_peaks_annotation_cut.txt; export PATH=$PATH:/opt/miniconda3/envs/utap/bin; annotatePeaks.pl /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/12_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_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/12_peaks_annotation/report_annotation_homer.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/12_peaks_annotation_peaks.txt [Tue Nov 19 06:01:03 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=4034, disk_mb=4034, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:24:10 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_Het2/Aire_C313Y_Het2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/2_fastqc.Aire_C313Y_Het2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het2 threads: 5 resources: mem_mb=4034, disk_mb=4034, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_Het2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_Het2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_Het2/Aire_C313Y_Het2_R2.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/2_fastqc.Aire_C313Y_Het2.txt 2>&1 [Tue Nov 19 05:25:53 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=7724, disk_mb=7724, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 06:04:41 2024] rule rule_8_ngs_plot: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/8_ngs_plot/samples_genebody.avgprof.pdf log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/8_ngs_plot_genbody_pdf.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/8_ngs_plot_tss_pdf.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/8_ngs_plot_genbody_png.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/8_ngs_plot_tss_png.txt jobid: 0 reason: Forced execution threads: 20 resources: mem_mb=7724, disk_mb=7724, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 [Tue Nov 19 06:06:57 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=15000, mem_mb_total=15000 Select jobs to execute... [Tue Nov 19 05:59:12 2024] rule rule_10_tss_count: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free_shift.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT1_sorted.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT1_tss_counts.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_sort.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_counting.Aire_C313Y_WT1.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=15000, mem_mb_total=15000 sort -k1,1 -k2,2n /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free_shift.bed > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT1_sorted.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_sort.Aire_C313Y_WT1.txt /opt/miniconda3/envs/utap/bin/bedtools coverage -counts -sorted -a /home/labs/bioservices/services/UTAP-data/utap-meta-data/genomes/Mus_musculus/UCSC/mm10/mm10.TSS_+500_-500_uniqueProm.bed -b /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT1_sorted.bed > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT1_tss_counts.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_counting.Aire_C313Y_WT1.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT1_sorted.bed.deleted [Tue Nov 19 05:59:17 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=15000, mem_mb_total=15000 Select jobs to execute... [Tue Nov 19 05:31:08 2024] rule rule_10_tss_count: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free_shift.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT2_sorted.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT2_tss_counts.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_sort.Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_counting.Aire_C313Y_WT2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=15000, mem_mb_total=15000 sort -k1,1 -k2,2n /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free_shift.bed > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT2_sorted.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_sort.Aire_C313Y_WT2.txt /opt/miniconda3/envs/utap/bin/bedtools coverage -counts -sorted -a /home/labs/bioservices/services/UTAP-data/utap-meta-data/genomes/Mus_musculus/UCSC/mm10/mm10.TSS_+500_-500_uniqueProm.bed -b /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT2_sorted.bed > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT2_tss_counts.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_counting.Aire_C313Y_WT2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_WT2_sorted.bed.deleted [Tue Nov 19 05:31:21 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=15000, mem_mb_total=15000 Select jobs to execute... [Tue Nov 19 05:41:51 2024] rule rule_10_tss_count: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free_shift.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het3_sorted.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het3_tss_counts.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_sort.Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_counting.Aire_C313Y_Het3.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het3 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=15000, mem_mb_total=15000 sort -k1,1 -k2,2n /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het3_nucl_free_shift.bed > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het3_sorted.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_sort.Aire_C313Y_Het3.txt /opt/miniconda3/envs/utap/bin/bedtools coverage -counts -sorted -a /home/labs/bioservices/services/UTAP-data/utap-meta-data/genomes/Mus_musculus/UCSC/mm10/mm10.TSS_+500_-500_uniqueProm.bed -b /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het3_sorted.bed > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het3_tss_counts.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_counting.Aire_C313Y_Het3.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het3_sorted.bed.deleted [Tue Nov 19 05:42:11 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=15000, mem_mb_total=15000 Select jobs to execute... [Tue Nov 19 05:32:09 2024] rule rule_10_tss_count: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free_shift.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het2_sorted.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het2_tss_counts.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_sort.Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_counting.Aire_C313Y_Het2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=15000, mem_mb_total=15000 sort -k1,1 -k2,2n /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_Het2_nucl_free_shift.bed > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het2_sorted.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_sort.Aire_C313Y_Het2.txt /opt/miniconda3/envs/utap/bin/bedtools coverage -counts -sorted -a /home/labs/bioservices/services/UTAP-data/utap-meta-data/genomes/Mus_musculus/UCSC/mm10/mm10.TSS_+500_-500_uniqueProm.bed -b /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het2_sorted.bed > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het2_tss_counts.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/10_tss_count_counting.Aire_C313Y_Het2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/10_tss_count/Aire_C313Y_Het2_sorted.bed.deleted [Tue Nov 19 05:32:21 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=1278, disk_mb=1278, mem_mb_per_thread=25000, mem_mb_total=25000 Select jobs to execute... [Tue Nov 19 05:58:39 2024] rule rule_9_picard_plot: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1.pdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1.png, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1_nucl_free.pdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1_nucl_free.png log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_pdf_Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_png_Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_pdf_Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_png_Aire_C313Y_WT1.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT1 resources: mem_mb=1278, disk_mb=1278, tmpdir=/tmp, mem_mb_per_thread=25000, mem_mb_total=25000 (PATH=$PATH:/opt/miniconda3/envs/utap/bin; export HOME=$HOME; /opt/miniconda3/envs/utap/bin/picard CollectInsertSizeMetrics I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam MINIMUM_PCT=0.5 O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1.hist H=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1.pdf W=1000 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_pdf_Aire_C313Y_WT1.txt 2>&1 & /opt/miniconda3/envs/utap/bin/picard CollectInsertSizeMetrics I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.bam MINIMUM_PCT=0.5 O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1_nucl_free.hist H=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1_nucl_free.pdf W=1000 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_pdf_Aire_C313Y_WT1.txt 2>&1 & wait) && /opt/miniconda3/envs/utap/bin/gs -dNOPAUSE -dBATCH -sDEVICE=pngalpha -sOutputFile=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1.png -r144 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1.pdf > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_png_Aire_C313Y_WT1.txt 2>&1; /opt/miniconda3/envs/utap/bin/gs -dNOPAUSE -dBATCH -sDEVICE=pngalpha -sOutputFile=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1_nucl_free.png -r144 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT1_nucl_free.pdf > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_png_Aire_C313Y_WT1.txt 2>&1; [Tue Nov 19 05:59:21 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=2243, disk_mb=2243, mem_mb_per_thread=25000, mem_mb_total=25000 Select jobs to execute... [Tue Nov 19 05:29:58 2024] rule rule_9_picard_plot: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2.pdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2.png, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2_nucl_free.pdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2_nucl_free.png log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_pdf_Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_png_Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_pdf_Aire_C313Y_WT2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_png_Aire_C313Y_WT2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT2 resources: mem_mb=2243, disk_mb=2243, tmpdir=/tmp, mem_mb_per_thread=25000, mem_mb_total=25000 (PATH=$PATH:/opt/miniconda3/envs/utap/bin; export HOME=$HOME; /opt/miniconda3/envs/utap/bin/picard CollectInsertSizeMetrics I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT2_rm_dup.bam MINIMUM_PCT=0.5 O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2.hist H=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2.pdf W=1000 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_pdf_Aire_C313Y_WT2.txt 2>&1 & /opt/miniconda3/envs/utap/bin/picard CollectInsertSizeMetrics I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT2_nucl_free.bam MINIMUM_PCT=0.5 O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2_nucl_free.hist H=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2_nucl_free.pdf W=1000 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_pdf_Aire_C313Y_WT2.txt 2>&1 & wait) && /opt/miniconda3/envs/utap/bin/gs -dNOPAUSE -dBATCH -sDEVICE=pngalpha -sOutputFile=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2.png -r144 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2.pdf > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_png_Aire_C313Y_WT2.txt 2>&1; /opt/miniconda3/envs/utap/bin/gs -dNOPAUSE -dBATCH -sDEVICE=pngalpha -sOutputFile=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2_nucl_free.png -r144 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_WT2_nucl_free.pdf > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_png_Aire_C313Y_WT2.txt 2>&1; [Tue Nov 19 05:30:55 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=1952, disk_mb=1952, mem_mb_per_thread=25000, mem_mb_total=25000 Select jobs to execute... [Tue Nov 19 05:40:42 2024] rule rule_9_picard_plot: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3.pdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3.png, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3_nucl_free.pdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3_nucl_free.png log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_pdf_Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_png_Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_pdf_Aire_C313Y_Het3.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_png_Aire_C313Y_Het3.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het3 resources: mem_mb=1952, disk_mb=1952, tmpdir=/tmp, mem_mb_per_thread=25000, mem_mb_total=25000 (PATH=$PATH:/opt/miniconda3/envs/utap/bin; export HOME=$HOME; /opt/miniconda3/envs/utap/bin/picard CollectInsertSizeMetrics I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het3_rm_dup.bam MINIMUM_PCT=0.5 O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3.hist H=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3.pdf W=1000 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_pdf_Aire_C313Y_Het3.txt 2>&1 & /opt/miniconda3/envs/utap/bin/picard CollectInsertSizeMetrics I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het3_nucl_free.bam MINIMUM_PCT=0.5 O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3_nucl_free.hist H=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3_nucl_free.pdf W=1000 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_pdf_Aire_C313Y_Het3.txt 2>&1 & wait) && /opt/miniconda3/envs/utap/bin/gs -dNOPAUSE -dBATCH -sDEVICE=pngalpha -sOutputFile=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3.png -r144 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3.pdf > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_png_Aire_C313Y_Het3.txt 2>&1; /opt/miniconda3/envs/utap/bin/gs -dNOPAUSE -dBATCH -sDEVICE=pngalpha -sOutputFile=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3_nucl_free.png -r144 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het3_nucl_free.pdf > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_png_Aire_C313Y_Het3.txt 2>&1; [Tue Nov 19 05:41:21 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=2252, disk_mb=2252, mem_mb_per_thread=25000, mem_mb_total=25000 Select jobs to execute... [Tue Nov 19 05:28:58 2024] rule rule_9_picard_plot: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2.pdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2.png, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2_nucl_free.pdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2_nucl_free.png log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_pdf_Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_png_Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_pdf_Aire_C313Y_Het2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_png_Aire_C313Y_Het2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_Het2 resources: mem_mb=2252, disk_mb=2252, tmpdir=/tmp, mem_mb_per_thread=25000, mem_mb_total=25000 (PATH=$PATH:/opt/miniconda3/envs/utap/bin; export HOME=$HOME; /opt/miniconda3/envs/utap/bin/picard CollectInsertSizeMetrics I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_Het2_rm_dup.bam MINIMUM_PCT=0.5 O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2.hist H=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2.pdf W=1000 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_pdf_Aire_C313Y_Het2.txt 2>&1 & /opt/miniconda3/envs/utap/bin/picard CollectInsertSizeMetrics I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_Het2_nucl_free.bam MINIMUM_PCT=0.5 O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2_nucl_free.hist H=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2_nucl_free.pdf W=1000 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_pdf_Aire_C313Y_Het2.txt 2>&1 & wait) && /opt/miniconda3/envs/utap/bin/gs -dNOPAUSE -dBATCH -sDEVICE=pngalpha -sOutputFile=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2.png -r144 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2.pdf > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_png_Aire_C313Y_Het2.txt 2>&1; /opt/miniconda3/envs/utap/bin/gs -dNOPAUSE -dBATCH -sDEVICE=pngalpha -sOutputFile=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2_nucl_free.png -r144 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/9_picard_plot/Aire_C313Y_Het2_nucl_free.pdf > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/9_picard_nucl_free_png_Aire_C313Y_Het2.txt 2>&1; [Tue Nov 19 05:29:43 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=3000, mem_mb_total=3000 Select jobs to execute... [Tue Nov 19 05:59:12 2024] rule rule_11_call_peak_without_control: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free_shift.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT1_peaks.broadPeak/Aire_C313Y_WT1_peaks.broadPeak, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT1_peaks.broadPeak/Aire_C313Y_WT1_peaks_filtered.broadPeak log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_WT1.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=3000 /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free_shift.bed --bw 120 -B -f BEDPE --SPMR -B -g mm --nomodel -n Aire_C313Y_WT1 --shift -50 --extsize 100 --broad --keep-dup all -q 0.05 --outdir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT1_peaks.broadPeak > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_WT1.txt 2>&1 & wait /opt/miniconda3/envs/utap/bin/bedtools intersect -a /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT1_peaks.broadPeak/Aire_C313Y_WT1_peaks.broadPeak -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_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT1_peaks.broadPeak/Aire_C313Y_WT1_peaks_filtered.broadPeak 2>> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_WT1.txt [Tue Nov 19 05:59:39 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=1000, mem_mb_total=1000 Select jobs to execute... [Tue Nov 19 05:32:30 2024] rule rule_3_multiqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_WT1/Aire_C313Y_WT1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_WT2/Aire_C313Y_WT2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_Het3/Aire_C313Y_Het3_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc/Aire_C313Y_Het2/Aire_C313Y_Het2_R1_fastqc/fastqc_data.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/3_multiqc/multiqc_report.html log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/3_multiqc.txt jobid: 0 reason: Forced execution resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=1000, mem_mb_total=1000 /opt/miniconda3/envs/utap/bin/multiqc -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/3_multiqc /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/2_fastqc > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/3_multiqc.txt 2>&1 [Tue Nov 19 05:32:43 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:58:40 2024] rule rule_7_shift_bam: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free_shift.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_bam2bed.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_shift_bam.Aire_C313Y_WT1.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT1 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 /opt/miniconda3/envs/utap/bin/bedtools bamtobed -i /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_bam2bed.Aire_C313Y_WT1.txt && cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free.bed | awk -F $' ' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' >| /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free_shift.bed 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/7_shift_bam_shift_bam.Aire_C313Y_WT1.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT1_nucl_free.bed.deleted [Tue Nov 19 05:58:48 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=1040, disk_mb=1040, mem_mb_per_thread=100, mem_mb_total=100 Select jobs to execute... [Tue Nov 19 05:57:37 2024] rule rule_6_nucleosome_free: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.sam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.statistics log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_header.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_sam2bam.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_index.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_statistics.Aire_C313Y_WT1.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT1 resources: mem_mb=1040, disk_mb=1040, tmpdir=/tmp, mem_mb_per_thread=100, mem_mb_total=100 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.sam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_header.Aire_C313Y_WT1.txt /opt/miniconda3/envs/utap/bin/samtools view /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam | awk -F " " '{if (($9 > -120) && ($9 < 120)) print $_}' >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.sam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free.Aire_C313Y_WT1.txt /opt/miniconda3/envs/utap/bin/samtools view -h -b /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_sam2bam.Aire_C313Y_WT1.txt /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_index.Aire_C313Y_WT1.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.statistics 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/6_nucleosome_free_statistics.Aire_C313Y_WT1.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/6_nucleosome_free/Aire_C313Y_WT1_nucl_free.sam.deleted [Tue Nov 19 05:58:11 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=42647, disk_mb=42647, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Tue Nov 19 05:39:25 2024] rule rule_5_process_alignment: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT1.sam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_mito.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_not_uniq.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_sorted.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito_stat.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq_stat.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_sort.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_index.Aire_C313Y_WT1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup_stat.Aire_C313Y_WT1.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT1 threads: 5 resources: mem_mb=42647, disk_mb=42647, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 grep -v 'chrM' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT1.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_mito.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito.Aire_C313Y_WT1.txt /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_mito.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_mito_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_mito_stat.Aire_C313Y_WT1.txt /opt/miniconda3/envs/utap/bin/samtools view -q 39 -b -h -F 4 -f 0x2 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_mito.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_not_uniq.bam 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq.Aire_C313Y_WT1.txt /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_not_uniq.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_not_uniq_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_not_uniq_stat.Aire_C313Y_WT1.txt /opt/miniconda3/envs/utap/bin/picard SortSam SO=coordinate I=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_not_uniq.bam O=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_sorted.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_sort.Aire_C313Y_WT1.txt 2>&1 /opt/miniconda3/envs/utap/bin/picard MarkDuplicates INPUT=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_sorted.bam OUTPUT=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam M=/home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup_metrics.txt REMOVE_DUPLICATES=true > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup.Aire_C313Y_WT1.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_index.Aire_C313Y_WT1.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools flagstat /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_dup_statistics.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/5_proc_align_rm_dup_stat.Aire_C313Y_WT1.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_mito.bam.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_rm_not_uniq.bam.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/5_process_alignment/Aire_C313Y_WT1_sorted.bam.deleted [Tue Nov 19 05:57:19 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5468, disk_mb=5468, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:19:32 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT1.sam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/4_mapping.Aire_C313Y_WT1.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT1 threads: 20 resources: mem_mb=5468, disk_mb=5468, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie2 -X 2000 --local -p 20 -x /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 -1 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R1.fastq.gz -2 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R2.fastq.gz -S /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT1.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT1.stat 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/4_mapping/Aire_C313Y_WT1.sam.deleted [Tue Nov 19 05:39:06 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6163, disk_mb=6163, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:47:48 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_WT1/Aire_C313Y_WT1_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_WT1/Aire_C313Y_WT1_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R2.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/1_cutadapt.Aire_C313Y_WT1.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT1 threads: 4 resources: mem_mb=6163, disk_mb=6163, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 #Running in parallel is not supported on Python 2 /opt/miniconda3/envs/utap/bin/cutadapt -q 25 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGAGTGTAGATCTCGGTGGTCGCCGTATCATT --minimum-length 30 -j 4 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R1.fastq.gz -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R2.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_WT1/Aire_C313Y_WT1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/fastq/Aire_C313Y_WT1/Aire_C313Y_WT1_R2.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/1_cutadapt.Aire_C313Y_WT1.txt; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R1.fastq.gz.deleted /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/1_cutadapt/Aire_C313Y_WT1/Aire_C313Y_WT1_R2.fastq.gz.deleted [Tue Nov 19 04:51:56 2024] Finished job 0. 1 of 1 steps (100%) done ['Aire_C313Y_WT1', 'Aire_C313Y_WT2', 'Aire_C313Y_Het3', 'Aire_C313Y_Het2'] {} None None 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=3000, mem_mb_total=3000 Select jobs to execute... [Tue Nov 19 05:29:32 2024] rule rule_11_call_peak_without_control: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free_shift.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT2_peaks.broadPeak/Aire_C313Y_WT2_peaks.broadPeak, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT2_peaks.broadPeak/Aire_C313Y_WT2_peaks_filtered.broadPeak log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_WT2.txt jobid: 0 reason: Forced execution wildcards: sample=Aire_C313Y_WT2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=3000 /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/7_shift_bam/Aire_C313Y_WT2_nucl_free_shift.bed --bw 120 -B -f BEDPE --SPMR -B -g mm --nomodel -n Aire_C313Y_WT2 --shift -50 --extsize 100 --broad --keep-dup all -q 0.05 --outdir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT2_peaks.broadPeak > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_WT2.txt 2>&1 & wait /opt/miniconda3/envs/utap/bin/bedtools intersect -a /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT2_peaks.broadPeak/Aire_C313Y_WT2_peaks.broadPeak -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_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/11_call_peak/Aire_C313Y_WT2_peaks.broadPeak/Aire_C313Y_WT2_peaks_filtered.broadPeak 2>> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ATAC-seq_mm10/demo_AIRE/20241119_044729_data_for_demo_production_ATAC-Seq/logs_20241119_044729/11_call_peak.Aire_C313Y_WT2.txt [Tue Nov 19 05:31:27 2024] Finished job 0. 1 of 1 steps (100%) done