### Pipeline run code and environment: * Command: `/scratch/jps3dp/tools/databio//pepatac/pipelines/pepatac.py --sample-name gold3 --genome hg38 --input /project/shefflab/data/sra_fastq//SRR5210398_1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//pepatac/gold_atac/results_pipeline -P 32 -M 24000 --input2 /project/shefflab/data/sra_fastq//SRR5210398_2.fastq.gz --genome-size hs --trimmer skewer --prealignments rCRSd human_repeats --deduplicator samblaster --blacklist /nv/t1/genomes//hg38/blacklist/default/hg38_blacklist.bed.gz --peak-type fixed --extend 250 --frip-ref-peaks None` * Compute host: udc-aj37-15c1 * Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/pepatac * Outfolder: /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/ * Pipeline started at: (09-14 14:34:38) elapsed: 31.0 _TIME_ ### Version log: * Python version: 3.7.4 * Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.7/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/pepatac/pipelines` * Pipeline version: 0.9.5 * Pipeline hash: 9d04c5b9b64523ab57a715a490430311eef462bb * Pipeline branch: * master * Pipeline date: 2020-09-08 11:15:59 -0400 * Pipeline diff: 3 files changed, 8 insertions(+), 7 deletions(-) ### Arguments passed to pipeline: * `TSS_name`: `None` * `aligner`: `bowtie2` * `anno_name`: `None` * `blacklist`: `/nv/t1/genomes//hg38/blacklist/default/hg38_blacklist.bed.gz` * `config_file`: `pepatac.yaml` * `cores`: `32` * `deduplicator`: `samblaster` * `dirty`: `False` * `extend`: `250` * `force_follow`: `False` * `frip_ref_peaks`: `None` * `genome_assembly`: `hg38` * `genome_size`: `hs` * `input`: `['/project/shefflab/data/sra_fastq//SRR5210398_1.fastq.gz']` * `input2`: `['/project/shefflab/data/sra_fastq//SRR5210398_2.fastq.gz']` * `keep`: `False` * `lite`: `False` * `logdev`: `False` * `mem`: `24000` * `motif`: `False` * `new_start`: `False` * `no_fifo`: `False` * `no_scale`: `False` * `output_parent`: `/project/shefflab/processed//pepatac/gold_atac/results_pipeline` * `paired_end`: `True` * `peak_caller`: `macs2` * `peak_type`: `fixed` * `prealignments`: `['rCRSd', 'human_repeats']` * `prioritize`: `False` * `recover`: `False` * `sample_name`: `gold3` * `silent`: `False` * `single_or_paired`: `PAIRED` * `skipqc`: `False` * `sob`: `False` * `testmode`: `False` * `trimmer`: `skewer` * `verbosity`: `None` ---------------------------------------- Local input file: /project/shefflab/data/sra_fastq//SRR5210398_1.fastq.gz Local input file: /project/shefflab/data/sra_fastq//SRR5210398_2.fastq.gz > `File_mb` 4809 2 _RES_ > `Read_type` PAIRED PEPATAC _RES_ > `Genome` hg38 PEPATAC _RES_ ### Merge/link and fastq conversion: (09-14 14:34:38) elapsed: 1.0 _TIME_ Number of input file sets: 2 Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R1.fastq.gz` > `ln -sf /project/shefflab/data/sra_fastq//SRR5210398_1.fastq.gz /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R1.fastq.gz` (40028)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 40028; Command: ln; Return code: 0; Memory used: 0.001GB Local input file: '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R1.fastq.gz' Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R2.fastq.gz` > `ln -sf /project/shefflab/data/sra_fastq//SRR5210398_2.fastq.gz /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R2.fastq.gz` (40069)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.002GB. PID: 40069; Command: ln; Return code: 0; Memory used: 0.002GB Local input file: '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R2.fastq.gz' Found .fastq.gz file Found .fq.gz file; no conversion necessary Found .fastq.gz file Found .fq.gz file; no conversion necessary ['ln -sf /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R1.fastq.gz /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1.fastq.gz', 'ln -sf /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R2.fastq.gz /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R2.fastq.gz'] Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1.fastq.gz`,`/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R2.fastq.gz` > `ln -sf /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R1.fastq.gz /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1.fastq.gz` (40109)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.002GB. PID: 40109; Command: ln; Return code: 0; Memory used: 0.002GB > `ln -sf /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/gold3_R2.fastq.gz /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R2.fastq.gz` (40151)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.002GB. PID: 40151; Command: ln; Return code: 0; Memory used: 0.002GB > `Raw_reads` 166092252 PEPATAC _RES_ > `Fastq_reads` 166092252 PEPATAC _RES_ ### Adapter trimming: (09-14 14:37:01) elapsed: 143.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1_trim.fastq` > `skewer -f sanger -t 32 -m pe -x /scratch/jps3dp/tools/databio//pepatac/tools/NexteraPE-PE.fa --quiet -o /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1.fastq.gz /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R2.fastq.gz` (41251)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container .--. .-. : .--': :.-. `. `. : `'.' .--. .-..-..-. .--. .--. _`, :: . `.' '_.': `; `; :' '_.': ..' `.__.':_;:_;`.__.'`.__.__.'`.__.':_; skewer v0.2.2 [April 4, 2016] Parameters used: -- 3' end adapter sequences in file (-x): /scratch/jps3dp/tools/databio//pepatac/tools/NexteraPE-PE.fa A: [0;33mAGATGTGTATAAGAGACAG [0mB: [0;33mAGATGTGTATAAGAGACAG [0mC: [0;33mTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG [0mD: [0;33mCTGTCTCTTATACACATCTGACGCTGCCGACGA [0mE: [0;33mGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG [0mF: [0;33mCTGTCTCTTATACACATCTCCGAGCCCACGAGA [0m-- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 32 Mon Sep 14 14:37:01 2020[0;32m >> started[0m Mon Sep 14 14:39:28 2020[0;32m >> done[0m (146.701s) 83046126 read pairs processed; of these: 556 ( 0.00%) short read pairs filtered out after trimming by size control 276 ( 0.00%) empty read pairs filtered out after trimming by size control 83045294 (100.00%) read pairs available; of these: 3119403 ( 3.76%) trimmed read pairs available after processing 79925891 (96.24%) untrimmed read pairs available after processing log has been saved to "/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3-trimmed.log".Command completed. Elapsed time: 0:02:27. Running peak memory: 0.048GB. PID: 41251; Command: skewer; Return code: 0; Memory used: 0.048GB > `mv /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3-trimmed-pair1.fastq /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1_trim.fastq` (41613)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.048GB. PID: 41613; Command: mv; Return code: 0; Memory used: 0.001GB > `mv /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3-trimmed-pair2.fastq /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R2_trim.fastq` (41614)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.048GB. PID: 41614; Command: mv; Return code: 0; Memory used: 0.0GB Evaluating read trimming > `Trimmed_reads` 166090588 PEPATAC _RES_ > `Trim_loss_rate` 0.0 PEPATAC _RES_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1_trim_fastqc.html` > `fastqc --noextract --outdir /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastqc /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1_trim.fastq` (41754)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container Started analysis of gold3_R1_trim.fastq Approx 5% complete for gold3_R1_trim.fastq Approx 10% complete for gold3_R1_trim.fastq Approx 15% complete for gold3_R1_trim.fastq Approx 20% complete for gold3_R1_trim.fastq Approx 25% complete for gold3_R1_trim.fastq Approx 30% complete for gold3_R1_trim.fastq Approx 35% complete for gold3_R1_trim.fastq Approx 40% complete for gold3_R1_trim.fastq Approx 45% complete for gold3_R1_trim.fastq Approx 50% complete for gold3_R1_trim.fastq Approx 55% complete for gold3_R1_trim.fastq Approx 60% complete for gold3_R1_trim.fastq Approx 65% complete for gold3_R1_trim.fastq Approx 70% complete for gold3_R1_trim.fastq Approx 75% complete for gold3_R1_trim.fastq Approx 80% complete for gold3_R1_trim.fastq Approx 85% complete for gold3_R1_trim.fastq Approx 90% complete for gold3_R1_trim.fastq Approx 95% complete for gold3_R1_trim.fastq Analysis complete for gold3_R1_trim.fastqCommand completed. Elapsed time: 0:03:22. Running peak memory: 0.255GB. PID: 41754; Command: fastqc; Return code: 0; Memory used: 0.255GB > `FastQC report r1` fastq/gold3_R1_trim_fastqc.html FastQC report r1 None PEPATAC _OBJ_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R2_trim_fastqc.html` > `fastqc --noextract --outdir /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastqc /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R2_trim.fastq` (42317)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container Started analysis of gold3_R2_trim.fastq Approx 5% complete for gold3_R2_trim.fastq Approx 10% complete for gold3_R2_trim.fastq Approx 15% complete for gold3_R2_trim.fastq Approx 20% complete for gold3_R2_trim.fastq Approx 25% complete for gold3_R2_trim.fastq Approx 30% complete for gold3_R2_trim.fastq Approx 35% complete for gold3_R2_trim.fastq Approx 40% complete for gold3_R2_trim.fastq Approx 45% complete for gold3_R2_trim.fastq Approx 50% complete for gold3_R2_trim.fastq Approx 55% complete for gold3_R2_trim.fastq Approx 60% complete for gold3_R2_trim.fastq Approx 65% complete for gold3_R2_trim.fastq Approx 70% complete for gold3_R2_trim.fastq Approx 75% complete for gold3_R2_trim.fastq Approx 80% complete for gold3_R2_trim.fastq Approx 85% complete for gold3_R2_trim.fastq Approx 90% complete for gold3_R2_trim.fastq Approx 95% complete for gold3_R2_trim.fastq Analysis complete for gold3_R2_trim.fastqCommand completed. Elapsed time: 0:03:23. Running peak memory: 0.255GB. PID: 42317; Command: fastqc; Return code: 0; Memory used: 0.253GB > `FastQC report r2` fastq/gold3_R2_trim_fastqc.html FastQC report r2 None PEPATAC _OBJ_ ### Prealignments (09-14 14:46:28) elapsed: 567.0 _TIME_ Prealignment assemblies: ['rCRSd', 'human_repeats'] ### Map to rCRSd (09-14 14:46:28) elapsed: 0.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/rCRSd_bt2` > `mkfifo /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/rCRSd_bt2` (42798)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.255GB. PID: 42798; Command: mkfifo; Return code: 0; Memory used: 0.017GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_bt_aln_summary.log`,`/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R2.fq.gz` > `perl /scratch/jps3dp/tools/databio//pepatac/tools/filter_paired_fq.pl /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/rCRSd_bt2 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1_trim.fastq /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R2_trim.fastq /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R1.fq /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R2.fq` (42840)
Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_bt_aln_summary.log`,`/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R2.fq.gz` > `(bowtie2 -p 32 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/rCRSd/bowtie2_index/default/rCRSd --rg-id gold3 -U /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3_R1_trim.fastq --un /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/rCRSd_bt2 > /dev/null) 2>/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_bt_aln_summary.log` (42841)
not gzipping outputCommand completed. Elapsed time: 0:11:16. Running peak memory: 0.255GB. PID: 42841; Command: bowtie2; Return code: 0; Memory used: 0.138GB > `grep 'aligned exactly 1 time' /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_bt_aln_summary.log | awk '{print $1}'` > `Aligned_reads_rCRSd` 29229450.0 PEPATAC _RES_ > `Alignment_rate_rCRSd` 17.6 PEPATAC _RES_ ### Map to human_repeats (09-14 14:57:50) elapsed: 682.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/human_repeats_bt2` > `mkfifo /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/human_repeats_bt2` (44155)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.255GB. PID: 44155; Command: mkfifo; Return code: 0; Memory used: 0.002GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_bt_aln_summary.log`,`/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R2.fq.gz` > `perl /scratch/jps3dp/tools/databio//pepatac/tools/filter_paired_fq.pl /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/human_repeats_bt2 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R1.fq /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R2.fq /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R1.fq /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R2.fq` (44196)
Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_bt_aln_summary.log`,`/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R2.fq.gz` > `(bowtie2 -p 32 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_repeats/bowtie2_index/default/human_repeats --rg-id gold3 -U /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R1.fq --un /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/human_repeats_bt2 > /dev/null) 2>/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_bt_aln_summary.log` (44197)
not gzipping output 14614725 reads skipped 0 reads lostCommand completed. Elapsed time: 0:10:02. Running peak memory: 0.255GB. PID: 44197; Command: bowtie2; Return code: 0; Memory used: 0.156GB > `grep 'aligned exactly 1 time' /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_bt_aln_summary.log | awk '{print $1}'` > `Aligned_reads_human_repeats` 10699930.0 PEPATAC _RES_ > `Alignment_rate_human_repeats` 6.44 PEPATAC _RES_ ### Compress all unmapped read files (09-14 15:07:52) elapsed: 602.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R1.fq.gz` > `pigz -f -p 32 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R1.fq` (45506)
5349965 reads skipped 0 reads lostCommand completed. Elapsed time: 0:00:28. Running peak memory: 0.255GB. PID: 45506; Command: pigz; Return code: 0; Memory used: 0.048GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R2.fq.gz` > `pigz -f -p 32 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_rCRSd_unmap_R2.fq` (45609)
Command completed. Elapsed time: 0:00:35. Running peak memory: 0.255GB. PID: 45609; Command: pigz; Return code: 0; Memory used: 0.047GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R1.fq.gz` > `pigz -f -p 32 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R1.fq` (45716)
Command completed. Elapsed time: 0:00:30. Running peak memory: 0.255GB. PID: 45716; Command: pigz; Return code: 0; Memory used: 0.048GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R2.fq.gz` > `pigz -f -p 32 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R2.fq` (45822)
Command completed. Elapsed time: 0:00:45. Running peak memory: 0.255GB. PID: 45822; Command: pigz; Return code: 0; Memory used: 0.045GB ### Map to genome (09-14 15:10:09) elapsed: 137.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam` > `bowtie2 -p 32 --very-sensitive -X 2000 --rg-id gold3 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -1 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R1.fq.gz -2 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/gold3_human_repeats_unmap_R2.fq.gz | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/tmpxoy3eakj -o /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_temp.bam` (46202,46203,46205)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container 63080604 reads; of these: 63080604 (100.00%) were paired; of these: 2101698 (3.33%) aligned concordantly 0 times 51634611 (81.85%) aligned concordantly exactly 1 time 9344295 (14.81%) aligned concordantly >1 times ---- 2101698 pairs aligned concordantly 0 times; of these: 97320 (4.63%) aligned discordantly 1 time ---- 2004378 pairs aligned 0 times concordantly or discordantly; of these: 4008756 mates make up the pairs; of these: 2236283 (55.78%) aligned 0 times 1108801 (27.66%) aligned exactly 1 time 663672 (16.56%) aligned >1 times 98.23% overall alignment rate [bam_sort_core] merging from 31 files and 1 in-memory blocks...Command completed. Elapsed time: 0:38:22. Running peak memory: 4.119GB. PID: 46203; Command: samtools; Return code: 0; Memory used: 0.021GB PID: 46202; Command: bowtie2; Return code: 0; Memory used: 4.119GB PID: 46205; Command: samtools; Return code: 0; Memory used: 0.92GB > `samtools view -b -q 10 -@ 32 -U /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_fail_qc.bam -f 2 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_temp.bam > /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam` (50853)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:01:37. Running peak memory: 4.119GB. PID: 50853; Command: samtools; Return code: 0; Memory used: 0.053GB [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container > `Mapped_reads` 123924925 PEPATAC _RES_ > `QC_filtered_reads` 9613401 PEPATAC _RES_ > `Aligned_reads` 114311524 PEPATAC _RES_ > `Alignment_rate` 68.82 PEPATAC _RES_ > `Total_efficiency` 68.82 PEPATAC _RES_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam.bai` > `samtools index /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_temp.bam` (51443)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:00:34. Running peak memory: 4.119GB. PID: 51443; Command: samtools; Return code: 0; Memory used: 0.026GB > `samtools index /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam` (51515)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:00:30. Running peak memory: 4.119GB. PID: 51515; Command: samtools; Return code: 0; Memory used: 0.028GB Missing stat 'Mitochondrial_reads' > `samtools idxstats /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_temp.bam | grep -we 'chrM' -we 'ChrM' -we 'ChrMT' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd'| cut -f 3` [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container > `Mitochondrial_reads` 14199 PEPATAC _RES_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_noMT.bam` > `samtools idxstats /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam | cut -f 1-2 | awk '{print $1, 0, $2}' | grep -vwe 'chrM' -vwe 'ChrM' -vwe 'ChrMT' -vwe 'chrMT' -vwe 'M' -vwe 'MT' -vwe 'rCRSd' > /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/chr_sizes.bed` (51717,51718,51720,51727)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:00:00. Running peak memory: 4.119GB. PID: 51717; Command: samtools; Return code: 0; Memory used: 0.02GB PID: 51720; Command: awk; Return code: 0; Memory used: 0.018GB PID: 51718; Command: cut; Return code: 0; Memory used: 0.002GB PID: 51727; Command: grep; Return code: 0; Memory used: 0.018GB > `samtools view -L /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/chr_sizes.bed -b -@ 32 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam > /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_noMT.bam` (51882)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:00:52. Running peak memory: 4.119GB. PID: 51882; Command: samtools; Return code: 0; Memory used: 0.05GB > `mv /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_noMT.bam /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam` (52008)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.119GB. PID: 52008; Command: mv; Return code: 0; Memory used: 0.001GB > `samtools index /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam` (52010) [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Command completed. Elapsed time: 0:00:38. Running peak memory: 4.119GB. PID: 52010; Command: samtools; Return code: 0; Memory used: 0.026GB ### Calculate NRF, PBC1, and PBC2 (09-14 15:53:45) elapsed: 2616.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_bamQC.tsv` > `/scratch/jps3dp/tools/databio//pepatac/tools/bamQC.py -i /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam -c 32 -o /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_bamQC.tsv` (52086)
Registering input file: '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam' Temporary files will be stored in: '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/tmp_gold3_sort_h78e4gl8' Processing with 32 cores... Merging 153 files into output file: '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_bamQC.tsv'Command completed. Elapsed time: 0:01:43. Running peak memory: 6.249GB. PID: 52086; Command: /scratch/jps3dp/tools/databio//pepatac/tools/bamQC.py; Return code: 0; Memory used: 6.249GB > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_bamQC.tsv` > `NRF` 0.9 PEPATAC _RES_ > `PBC1` 0.95 PEPATAC _RES_ > `PBC2` 18.89 PEPATAC _RES_ Missing stat 'Unmapped_reads' Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_unmap.bam` > `samtools view -b -@ 32 -f 12 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_temp.bam > /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_unmap.bam` (52585)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:00:10. Running peak memory: 6.249GB. PID: 52585; Command: samtools; Return code: 0; Memory used: 0.03GB > `samtools view -c -f 4 -@ 32 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_temp.bam` [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container > `Unmapped_reads` 2236283 PEPATAC _RES_ ### Remove duplicates and produce signal tracks (09-14 15:55:48) elapsed: 123.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam` > `samtools sort -n -@ 8 -T /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/tmpuavzwnuf /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam | samtools view -h - -@ 8 | samblaster -r --ignoreUnmated 2> /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_dedup_metrics_log.txt | samtools view -b - -@ 8 | samtools sort - -@ 8 -T /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/tmpuavzwnuf -o /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam` (52751,52752,52754,52761,52772)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [bam_sort_core] merging from 24 files and 8 in-memory blocks... [bam_sort_core] merging from 24 files and 8 in-memory blocks...Command completed. Elapsed time: 0:05:12. Running peak memory: 7.491GB. PID: 52761; Command: samtools; Return code: 0; Memory used: 0.022GB PID: 52751; Command: samtools; Return code: 0; Memory used: 7.491GB PID: 52754; Command: samblaster; Return code: 0; Memory used: 1.055GB PID: 52752; Command: samtools; Return code: 0; Memory used: 0.02GB PID: 52772; Command: samtools; Return code: 0; Memory used: 7.087GB > `samtools index /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam` (53675)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:00:28. Running peak memory: 7.491GB. PID: 53675; Command: samtools; Return code: 0; Memory used: 0.027GB > `grep 'Removed' /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_dedup_metrics_log.txt | tr -s ' ' | cut -f 3 -d ' '` > `Duplicate_reads` 3152724 PEPATAC _RES_ > `Dedup_aligned_reads` 111158800.0 PEPATAC _RES_ > `Dedup_alignment_rate` 66.93 PEPATAC _RES_ > `Dedup_total_efficiency` 66.93 PEPATAC _RES_ Missing stat 'Read_length' > `samtools stats /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-` [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container > `Read_length` 40 PEPATAC _RES_ Missing stat 'Genome_size' > `awk '{sum+=$2} END {printf "%.0f", sum}' /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes` > `Genome_size` 3099922541 PEPATAC _RES_ ### Calculate library complexity (09-14 16:03:18) elapsed: 450.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_out.txt` > `preseq c_curve -v -o /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_out.txt -B /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam` (54235)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BAM_INPUT TOTAL READS = 57154185 COUNTS_SUM = 57154185 DISTINCT READS = 5.01862e+07 DISTINCT COUNTS = 144 MAX COUNT = 1463 COUNTS OF 1 = 4.51091e+07 OBSERVED COUNTS (1464) 1 45109121 2 4116003 3 592902 4 176092 5 79892 6 42081 7 24142 8 14823 9 9310 10 6185 11 4307 12 2848 13 2014 14 1505 15 1038 16 782 17 607 18 482 19 339 20 254 21 217 22 158 23 138 24 114 25 92 26 85 27 76 28 62 29 38 30 35 31 35 32 24 33 12 34 23 35 13 36 20 37 12 38 12 39 12 40 5 41 11 42 5 43 9 44 4 45 14 46 6 47 6 48 4 49 7 50 8 51 6 52 3 53 4 54 3 55 3 56 2 57 7 58 6 59 2 60 3 61 3 62 2 63 2 64 5 65 4 66 2 67 1 68 6 69 5 70 3 71 4 73 1 74 3 75 1 76 1 77 1 78 1 79 3 80 1 82 3 84 2 85 3 86 1 87 1 88 2 89 1 91 1 92 3 93 2 94 4 95 2 97 2 98 1 99 4 100 1 101 2 103 1 105 1 112 1 114 1 116 1 117 2 118 1 119 3 121 1 125 1 133 1 137 1 138 1 139 1 140 1 142 1 143 2 144 1 150 1 162 1 178 1 179 1 190 1 198 1 199 1 200 1 213 1 216 1 224 1 226 1 230 1 238 1 251 1 266 1 293 1 331 1 347 1 382 1 391 1 465 1 469 1 504 1 540 1 677 1 824 1 930 1 1452 1 1463 1 sample size: 1000000 sample size: 2000000 sample size: 3000000 sample size: 4000000 sample size: 5000000 sample size: 6000000 sample size: 7000000 sample size: 8000000 sample size: 9000000 sample size: 10000000 sample size: 11000000 sample size: 12000000 sample size: 13000000 sample size: 14000000 sample size: 15000000 sample size: 16000000 sample size: 17000000 sample size: 18000000 sample size: 19000000 sample size: 20000000 sample size: 21000000 sample size: 22000000 sample size: 23000000 sample size: 24000000 sample size: 25000000 sample size: 26000000 sample size: 27000000 sample size: 28000000 sample size: 29000000 sample size: 30000000 sample size: 31000000 sample size: 32000000 sample size: 33000000 sample size: 34000000 sample size: 35000000 sample size: 36000000 sample size: 37000000 sample size: 38000000 sample size: 39000000 sample size: 40000000 sample size: 41000000 sample size: 42000000 sample size: 43000000 sample size: 44000000 sample size: 45000000 sample size: 46000000 sample size: 47000000 sample size: 48000000 sample size: 49000000 sample size: 50000000 sample size: 51000000 sample size: 52000000 sample size: 53000000 sample size: 54000000 sample size: 55000000 sample size: 56000000 sample size: 57000000Command completed. Elapsed time: 0:12:53. Running peak memory: 7.491GB. PID: 54235; Command: preseq; Return code: 0; Memory used: 0.025GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_yield.txt` > `preseq lc_extrap -v -o /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_yield.txt -B /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam` (55776)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BAM_INPUT TOTAL READS = 57154185 DISTINCT READS = 5.01862e+07 DISTINCT COUNTS = 144 MAX COUNT = 1463 COUNTS OF 1 = 4.51091e+07 MAX TERMS = 70 OBSERVED COUNTS (1464) 1 45109121 2 4116003 3 592902 4 176092 5 79892 6 42081 7 24142 8 14823 9 9310 10 6185 11 4307 12 2848 13 2014 14 1505 15 1038 16 782 17 607 18 482 19 339 20 254 21 217 22 158 23 138 24 114 25 92 26 85 27 76 28 62 29 38 30 35 31 35 32 24 33 12 34 23 35 13 36 20 37 12 38 12 39 12 40 5 41 11 42 5 43 9 44 4 45 14 46 6 47 6 48 4 49 7 50 8 51 6 52 3 53 4 54 3 55 3 56 2 57 7 58 6 59 2 60 3 61 3 62 2 63 2 64 5 65 4 66 2 67 1 68 6 69 5 70 3 71 4 73 1 74 3 75 1 76 1 77 1 78 1 79 3 80 1 82 3 84 2 85 3 86 1 87 1 88 2 89 1 91 1 92 3 93 2 94 4 95 2 97 2 98 1 99 4 100 1 101 2 103 1 105 1 112 1 114 1 116 1 117 2 118 1 119 3 121 1 125 1 133 1 137 1 138 1 139 1 140 1 142 1 143 2 144 1 150 1 162 1 178 1 179 1 190 1 198 1 199 1 200 1 213 1 216 1 224 1 226 1 230 1 238 1 251 1 266 1 293 1 331 1 347 1 382 1 391 1 465 1 469 1 504 1 540 1 677 1 824 1 930 1 1452 1 1463 1 [ESTIMATING YIELD CURVE] [BOOTSTRAPPING HISTOGRAM] ...._.........__....._.._................_..._................._............_............._._...._..........._.._. [COMPUTING CONFIDENCE INTERVALS] [WRITING OUTPUT]Command completed. Elapsed time: 0:12:56. Running peak memory: 7.491GB. PID: 55776; Command: preseq; Return code: 0; Memory used: 0.024GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_counts.txt` > `echo '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam) > /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_counts.txt` (57074)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:00:57. Running peak memory: 7.491GB. PID: 57074; Command: echo; Return code: 0; Memory used: 0.021GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_plot.pdf`,`/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_plot.png` > `Rscript /scratch/jps3dp/tools/databio//pepatac/tools/PEPATAC.R preseq -i /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_yield.txt -r /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_counts.txt -o /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_plot` (57480)
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help Processing gold3 INFO: Found real counts for gold3 - Total (M): 114.30837 Unique (M): 108.002922 Library complexity plot completed!Command completed. Elapsed time: 0:00:23. Running peak memory: 7.491GB. PID: 57480; Command: Rscript; Return code: 0; Memory used: 0.135GB > `Library complexity` QC_hg38/gold3_preseq_plot.pdf Library complexity QC_hg38/gold3_preseq_plot.png PEPATAC _OBJ_ Missing stat 'Frac_exp_unique_at_10M' > `grep -w '^10000000' /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_preseq_yield.txt | awk '{print $2}'` > `Frac_exp_unique_at_10M` 0.9696 PEPATAC _RES_ ### Produce signal tracks (09-14 16:30:27) elapsed: 1629.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_exact.bw`,`/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_smooth.bw` > `/scratch/jps3dp/tools/databio//pepatac/tools/bamSitesToWig.py -i /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -e /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact -b /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_shift.bed -o /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_exact.bw -w /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_smooth.bw -m atac -p 21 --variable-step --scale 114311524.0` (57680)
Cutting parallel chroms in half to accommodate two tracks. Registering input file: '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam' Temporary files will be stored in: '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/tmp_gold3_sort_dedup_cuttrace_egmtzw48' Processing with 10 cores... 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doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount 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doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container Reduce step (merge files)... Merging 153 files into output file: '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_exact.bw' [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container Merging 153 files into output file: '/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_smooth.bw' [33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:12:52. Running peak memory: 7.491GB. PID: 57680; Command: /scratch/jps3dp/tools/databio//pepatac/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.46GB ### Calculate TSS enrichment (09-14 16:43:18) elapsed: 772.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_TSS_enrichment.txt` > `/scratch/jps3dp/tools/databio//pepatac/tools/pyTssEnrichment.py -a /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed -p ends -c 32 -z -v -s 6 -o /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_TSS_enrichment.txt` (92001)
Command completed. Elapsed time: 0:00:13. Running peak memory: 7.491GB. PID: 92001; Command: /scratch/jps3dp/tools/databio//pepatac/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.028GB Missing stat 'TSS_score' > `TSS_score` 11.0 PEPATAC _RES_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_TSS_enrichment.pdf` > `Rscript /scratch/jps3dp/tools/databio//pepatac/tools/PEPATAC.R tss -i /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_TSS_enrichment.txt` (92079)
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help Generating TSS plot with /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_TSS_enrichment.txt `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' TSS enrichment plot completed!Command completed. Elapsed time: 0:00:11. Running peak memory: 7.491GB. PID: 92079; Command: Rscript; Return code: 0; Memory used: 0.137GB > `TSS enrichment` QC_hg38/gold3_TSS_enrichment.pdf TSS enrichment QC_hg38/gold3_TSS_enrichment.png PEPATAC _OBJ_ ### Plot fragment distribution (09-14 16:43:43) elapsed: 24.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_fragLenDistribution.pdf` > `perl /scratch/jps3dp/tools/databio//pepatac/tools/fragment_length_dist.pl /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_sort_dedup.bam /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_fragLen.txt` (92182)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:04:16. Running peak memory: 7.491GB. PID: 92182; Command: perl; Return code: 0; Memory used: 0.021GB > `sort -n /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_fragLen.txt | uniq -c > /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_fragCount.txt` (92680,92681)
Command completed. Elapsed time: 0:00:21. Running peak memory: 7.491GB. PID: 92681; Command: uniq; Return code: 0; Memory used: 0.021GB PID: 92680; Command: sort; Return code: 0; Memory used: 3.828GB > `Rscript /scratch/jps3dp/tools/databio//pepatac/tools/PEPATAC.R frag -l /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_fragLen.txt -c /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_fragCount.txt -p /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_fragLenDistribution.pdf -t /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/QC_hg38/gold3_fragLenDistribution.txt` (92791)
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help Fragment distribution plot completed!Command completed. Elapsed time: 0:00:12. Running peak memory: 7.491GB. PID: 92791; Command: Rscript; Return code: 0; Memory used: 0.128GB > `Fragment distribution` QC_hg38/gold3_fragLenDistribution.pdf Fragment distribution QC_hg38/gold3_fragLenDistribution.png PEPATAC _OBJ_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/hg38_annotations.bed` > `ln -sf /project/shefflab/genomes/hg38/feat_annotation/default/hg38_annotations.bed.gz /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/hg38_annotations.bed.gz` (92909)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.491GB. PID: 92909; Command: ln; Return code: 0; Memory used: 0.01GB > `pigz -f -p 32 -d -c /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/hg38_annotations.bed.gz > /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/hg38_annotations.bed` (92950)
Command completed. Elapsed time: 0:00:02. Running peak memory: 7.491GB. PID: 92950; Command: pigz; Return code: 0; Memory used: 0.016GB ### Call peaks (09-14 16:48:34) elapsed: 291.0 _TIME_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38/gold3_peaks.narrowPeak` > `macs2 callpeak -t /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_shift.bed -f BED --outdir /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38 -n gold3 -g hs --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01` (92997)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 14 Sep 2020 16:48:41: # Command line: callpeak -t /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_shift.bed -f BED --outdir /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38 -n gold3 -g hs --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01 # ARGUMENTS LIST: # name = gold3 # format = BED # ChIP-seq file = ['/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_shift.bed'] # control file = None # effective genome size = 2.70e+09 # band width = 300 # model fold = [5, 50] # pvalue cutoff = 1.00e-02 # qvalue will not be calculated and reported as -1 in the final output. # The maximum gap between significant sites is assigned as the read length/tag size. # The minimum length of peaks is assigned as the predicted fragment length "d". # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off # Searching for subpeak summits is on INFO @ Mon, 14 Sep 2020 16:48:41: #1 read tag files... INFO @ Mon, 14 Sep 2020 16:48:41: #1 read treatment tags... INFO @ Mon, 14 Sep 2020 16:48:42: 1000000 INFO @ Mon, 14 Sep 2020 16:48:42: 2000000 INFO @ Mon, 14 Sep 2020 16:48:43: 3000000 INFO @ Mon, 14 Sep 2020 16:48:43: 4000000 INFO @ Mon, 14 Sep 2020 16:48:44: 5000000 INFO @ Mon, 14 Sep 2020 16:48:45: 6000000 INFO @ Mon, 14 Sep 2020 16:48:45: 7000000 INFO @ Mon, 14 Sep 2020 16:48:46: 8000000 INFO @ Mon, 14 Sep 2020 16:48:46: 9000000 INFO @ Mon, 14 Sep 2020 16:48:47: 10000000 INFO @ Mon, 14 Sep 2020 16:48:47: 11000000 INFO @ Mon, 14 Sep 2020 16:48:48: 12000000 INFO @ Mon, 14 Sep 2020 16:48:49: 13000000 INFO @ Mon, 14 Sep 2020 16:48:49: 14000000 INFO @ Mon, 14 Sep 2020 16:48:50: 15000000 INFO @ Mon, 14 Sep 2020 16:48:50: 16000000 INFO @ Mon, 14 Sep 2020 16:48:51: 17000000 INFO @ Mon, 14 Sep 2020 16:48:51: 18000000 INFO @ Mon, 14 Sep 2020 16:48:52: 19000000 INFO @ Mon, 14 Sep 2020 16:48:53: 20000000 INFO @ Mon, 14 Sep 2020 16:48:53: 21000000 INFO @ Mon, 14 Sep 2020 16:48:54: 22000000 INFO @ Mon, 14 Sep 2020 16:48:54: 23000000 INFO @ Mon, 14 Sep 2020 16:48:55: 24000000 INFO @ Mon, 14 Sep 2020 16:48:55: 25000000 INFO @ Mon, 14 Sep 2020 16:48:56: 26000000 INFO @ Mon, 14 Sep 2020 16:48:56: 27000000 INFO @ Mon, 14 Sep 2020 16:48:57: 28000000 INFO @ Mon, 14 Sep 2020 16:48:58: 29000000 INFO @ Mon, 14 Sep 2020 16:48:58: 30000000 INFO @ Mon, 14 Sep 2020 16:48:59: 31000000 INFO @ Mon, 14 Sep 2020 16:48:59: 32000000 INFO @ Mon, 14 Sep 2020 16:49:00: 33000000 INFO @ Mon, 14 Sep 2020 16:49:00: 34000000 INFO @ Mon, 14 Sep 2020 16:49:01: 35000000 INFO @ Mon, 14 Sep 2020 16:49:01: 36000000 INFO @ Mon, 14 Sep 2020 16:49:02: 37000000 INFO @ Mon, 14 Sep 2020 16:49:03: 38000000 INFO @ Mon, 14 Sep 2020 16:49:03: 39000000 INFO @ Mon, 14 Sep 2020 16:49:04: 40000000 INFO @ Mon, 14 Sep 2020 16:49:04: 41000000 INFO @ Mon, 14 Sep 2020 16:49:05: 42000000 INFO @ Mon, 14 Sep 2020 16:49:05: 43000000 INFO @ Mon, 14 Sep 2020 16:49:06: 44000000 INFO @ Mon, 14 Sep 2020 16:49:06: 45000000 INFO @ Mon, 14 Sep 2020 16:49:07: 46000000 INFO @ Mon, 14 Sep 2020 16:49:08: 47000000 INFO @ Mon, 14 Sep 2020 16:49:08: 48000000 INFO @ Mon, 14 Sep 2020 16:49:09: 49000000 INFO @ Mon, 14 Sep 2020 16:49:09: 50000000 INFO @ Mon, 14 Sep 2020 16:49:10: 51000000 INFO @ Mon, 14 Sep 2020 16:49:10: 52000000 INFO @ Mon, 14 Sep 2020 16:49:11: 53000000 INFO @ Mon, 14 Sep 2020 16:49:11: 54000000 INFO @ Mon, 14 Sep 2020 16:49:12: 55000000 INFO @ Mon, 14 Sep 2020 16:49:13: 56000000 INFO @ Mon, 14 Sep 2020 16:49:13: 57000000 INFO @ Mon, 14 Sep 2020 16:49:14: 58000000 INFO @ Mon, 14 Sep 2020 16:49:14: 59000000 INFO @ Mon, 14 Sep 2020 16:49:15: 60000000 INFO @ Mon, 14 Sep 2020 16:49:15: 61000000 INFO @ Mon, 14 Sep 2020 16:49:16: 62000000 INFO @ Mon, 14 Sep 2020 16:49:16: 63000000 INFO @ Mon, 14 Sep 2020 16:49:17: 64000000 INFO @ Mon, 14 Sep 2020 16:49:18: 65000000 INFO @ Mon, 14 Sep 2020 16:49:18: 66000000 INFO @ Mon, 14 Sep 2020 16:49:19: 67000000 INFO @ Mon, 14 Sep 2020 16:49:19: 68000000 INFO @ Mon, 14 Sep 2020 16:49:20: 69000000 INFO @ Mon, 14 Sep 2020 16:49:20: 70000000 INFO @ Mon, 14 Sep 2020 16:49:21: 71000000 INFO @ Mon, 14 Sep 2020 16:49:22: 72000000 INFO @ Mon, 14 Sep 2020 16:49:22: 73000000 INFO @ Mon, 14 Sep 2020 16:49:23: 74000000 INFO @ Mon, 14 Sep 2020 16:49:23: 75000000 INFO @ Mon, 14 Sep 2020 16:49:24: 76000000 INFO @ Mon, 14 Sep 2020 16:49:24: 77000000 INFO @ Mon, 14 Sep 2020 16:49:25: 78000000 INFO @ Mon, 14 Sep 2020 16:49:26: 79000000 INFO @ Mon, 14 Sep 2020 16:49:26: 80000000 INFO @ Mon, 14 Sep 2020 16:49:27: 81000000 INFO @ Mon, 14 Sep 2020 16:49:27: 82000000 INFO @ Mon, 14 Sep 2020 16:49:28: 83000000 INFO @ Mon, 14 Sep 2020 16:49:28: 84000000 INFO @ Mon, 14 Sep 2020 16:49:29: 85000000 INFO @ Mon, 14 Sep 2020 16:49:29: 86000000 INFO @ Mon, 14 Sep 2020 16:49:30: 87000000 INFO @ Mon, 14 Sep 2020 16:49:31: 88000000 INFO @ Mon, 14 Sep 2020 16:49:31: 89000000 INFO @ Mon, 14 Sep 2020 16:49:32: 90000000 INFO @ Mon, 14 Sep 2020 16:49:32: 91000000 INFO @ Mon, 14 Sep 2020 16:49:33: 92000000 INFO @ Mon, 14 Sep 2020 16:49:33: 93000000 INFO @ Mon, 14 Sep 2020 16:49:34: 94000000 INFO @ Mon, 14 Sep 2020 16:49:34: 95000000 INFO @ Mon, 14 Sep 2020 16:49:35: 96000000 INFO @ Mon, 14 Sep 2020 16:49:36: 97000000 INFO @ Mon, 14 Sep 2020 16:49:36: 98000000 INFO @ Mon, 14 Sep 2020 16:49:37: 99000000 INFO @ Mon, 14 Sep 2020 16:49:37: 100000000 INFO @ Mon, 14 Sep 2020 16:49:38: 101000000 INFO @ Mon, 14 Sep 2020 16:49:38: 102000000 INFO @ Mon, 14 Sep 2020 16:49:39: 103000000 INFO @ Mon, 14 Sep 2020 16:49:40: 104000000 INFO @ Mon, 14 Sep 2020 16:49:40: 105000000 INFO @ Mon, 14 Sep 2020 16:49:41: 106000000 INFO @ Mon, 14 Sep 2020 16:49:41: 107000000 INFO @ Mon, 14 Sep 2020 16:49:42: 108000000 INFO @ Mon, 14 Sep 2020 16:49:43: #1 tag size is determined as 50 bps INFO @ Mon, 14 Sep 2020 16:49:43: #1 tag size = 50.0 INFO @ Mon, 14 Sep 2020 16:49:43: #1 total tags in treatment: 108002827 INFO @ Mon, 14 Sep 2020 16:49:43: #1 finished! INFO @ Mon, 14 Sep 2020 16:49:43: #2 Build Peak Model... INFO @ Mon, 14 Sep 2020 16:49:43: #2 Skipped... INFO @ Mon, 14 Sep 2020 16:49:43: #2 Use 150 as fragment length INFO @ Mon, 14 Sep 2020 16:49:43: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) INFO @ Mon, 14 Sep 2020 16:49:43: #3 Call peaks... INFO @ Mon, 14 Sep 2020 16:49:43: # local lambda is disabled! INFO @ Mon, 14 Sep 2020 16:49:43: #3 !!!! DYNAMIC LAMBDA IS DISABLED !!!! INFO @ Mon, 14 Sep 2020 16:49:43: #3 Going to call summits inside each peak ... INFO @ Mon, 14 Sep 2020 16:49:43: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... INFO @ Mon, 14 Sep 2020 16:49:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 14 Sep 2020 16:51:11: #3 Call peaks for each chromosome... INFO @ Mon, 14 Sep 2020 16:53:52: #4 Write output xls file... /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38/gold3_peaks.xls INFO @ Mon, 14 Sep 2020 16:53:53: #4 Write peak in narrowPeak format file... /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38/gold3_peaks.narrowPeak INFO @ Mon, 14 Sep 2020 16:53:54: #4 Write summits bed file... /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38/gold3_summits.bed INFO @ Mon, 14 Sep 2020 16:53:55: Done!Command completed. Elapsed time: 0:05:21. Running peak memory: 7.491GB. PID: 92997; Command: macs2; Return code: 0; Memory used: 0.939GB > `Peak_count` 380540 PEPATAC _RES_ Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_shift.bed.gz` > `pigz -f -p 32 /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_shift.bed > /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38_exact/gold3_shift.bed.gz` (93765)
Command completed. Elapsed time: 0:00:08. Running peak memory: 7.491GB. PID: 93765; Command: pigz; Return code: 0; Memory used: 0.049GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38/gold3_peaks_fixedWidth.narrowPeak` > `awk -v OFS=' ' '{$2 = int(($3 - $2)/2 + $2 - 250); $3 = int($2 + 500); print}' /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38/gold3_peaks.narrowPeak > /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38/gold3_peaks_fixedWidth.narrowPeak` (93850)
Command completed. Elapsed time: 0:00:02. Running peak memory: 7.491GB. PID: 93850; Command: awk; Return code: 0; Memory used: 0.018GB Target to produce: `/project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38/gold3_peaks_normalized.narrowPeak` > `Rscript /scratch/jps3dp/tools/databio//pepatac/tools/PEPATAC.R reduce -i /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/peak_calling_hg38/gold3_peaks_fixedWidth.narrowPeak -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes --normalize` (93891)
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help Error in setorderv(final, cols = c("chr", "start")) : some columns are not in the data.table: chr,start Calls:Command completed. Elapsed time: 0:00:18. Running peak memory: 7.491GB. PID: 93891; Command: Rscript; Return code: 1; Memory used: 0.326GB Child process 42840 (perl) was already terminated. Child process 44196 (perl) was already terminated. Starting cleanup: 10 files; 3 conditional files for cleanup Cleaning up flagged intermediate files. . . Conditional flag found: [] These conditional files were left in place: - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/gold3*.fastq - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/*.fastq - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/fastq/*.log - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/tmphmrgfxyx - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/rCRSd_bt2 - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/tmpt5p4dcmz - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/prealignments/human_repeats_bt2 - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/tmpxoy3eakj - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_temp.bam.bai - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/chr_sizes.bed - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/gold3_temp.bam - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/aligned_hg38/tmpuavzwnuf - /project/shefflab/processed/pepatac/gold_atac/results_pipeline/gold3/raw/hg38_annotations.bed ### Pipeline failed at: (09-14 16:54:23) elapsed: 349.0 _TIME_ Total time: 2:20:16 Failure reason: Subprocess returned nonzero result. Check above output for details Traceback (most recent call last): File "/scratch/jps3dp/tools/databio//pepatac/pipelines/pepatac.py", line 2481, in-> setorderv Execution halted