### Pipeline run code and environment:
* Command: `/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/pipelines/pepatac.py --sample-name tutorial2 --genome hg38 --input /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial2_r1.fastq.gz --single-or-paired paired -O /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline -P 4 -M 8000 --input2 /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial2_r2.fastq.gz --genome-size hs --trimmer skewer --prealignments rCRSd human_repeats --deduplicator samblaster --peak-type fixed --extend 250 --frip-ref-peaks None`
* Compute host: udc-ba36-36
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac
* Outfolder: /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/
* Pipeline started at: (09-21 14:43:05) elapsed: 1.0 _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/data/tmp/pepatac_tutorial/tools/pepatac/pipelines`
* Pipeline version: 0.9.6
* Pipeline hash: ee6500ecf6fdc9cf3b1890635d7ee92206ddc58b
* Pipeline branch: * master
* Pipeline date: 2020-09-21 10:57:52 -0400
* Pipeline diff: 2 files changed, 9 insertions(+), 9 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `aligner`: `bowtie2`
* `anno_name`: `None`
* `blacklist`: `None`
* `config_file`: `pepatac.yaml`
* `cores`: `4`
* `deduplicator`: `samblaster`
* `dirty`: `False`
* `extend`: `250`
* `force_follow`: `False`
* `frip_ref_peaks`: `None`
* `genome_assembly`: `hg38`
* `genome_size`: `hs`
* `input`: `['/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial2_r1.fastq.gz']`
* `input2`: `['/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial2_r2.fastq.gz']`
* `keep`: `False`
* `lite`: `False`
* `logdev`: `False`
* `mem`: `8000`
* `motif`: `False`
* `new_start`: `False`
* `no_fifo`: `False`
* `no_scale`: `False`
* `output_parent`: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline`
* `paired_end`: `True`
* `peak_caller`: `macs2`
* `peak_type`: `fixed`
* `prealignments`: `['rCRSd', 'human_repeats']`
* `prioritize`: `False`
* `recover`: `False`
* `sample_name`: `tutorial2`
* `silent`: `False`
* `single_or_paired`: `paired`
* `skipqc`: `False`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `skewer`
* `verbosity`: `None`
----------------------------------------
['java', 'python', 'samtools', 'bedtools', 'bowtie2', 'fastqc', 'macs2', 'preseq', 'samblaster', 'skewer', 'perl', 'wigToBigWig', 'bigWigCat', 'bedToBigBed', 'bwa', 'fseq', '${TRIMMOMATIC}', '${PICARD}', 'pigz', 'Rscript', 'seqOutBias', 'bigWigMerge', 'bedGraphToBigWig']
Local input file: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial2_r1.fastq.gz
Local input file: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial2_r2.fastq.gz
> `File_mb` 27 2 _RES_
> `Read_type` paired PEPATAC _RES_
> `Genome` hg38 PEPATAC _RES_
### Merge/link and fastq conversion: (09-21 14:43:06) elapsed: 1.0 _TIME_
Number of input file sets: 2
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_R1.fastq.gz`
> `ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial2_r1.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_R1.fastq.gz` (9146)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 9146; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_R1.fastq.gz'
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_R2.fastq.gz`
> `ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial2_r2.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_R2.fastq.gz` (9147)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 9147; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_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 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_R1.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1.fastq.gz', 'ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_R2.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R2.fastq.gz']
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1.fastq.gz`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R2.fastq.gz`
> `ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_R1.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1.fastq.gz` (9148)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 9148; Command: ln; Return code: 0; Memory used: 0.0GB
> `ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/tutorial2_R2.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R2.fastq.gz` (9149)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 9149; Command: ln; Return code: 0; Memory used: 0.0GB
> `Raw_reads` 1000000 PEPATAC _RES_
> `Fastq_reads` 1000000 PEPATAC _RES_
### Adapter trimming: (09-21 14:43:08) elapsed: 3.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1_trim.fastq`
> `skewer -f sanger -t 4 -m pe -x /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/NexteraPE-PE.fa --quiet -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R2.fastq.gz` (9185)
Parameters used:
-- 3' end adapter sequences in file (-x): /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/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): 4
Mon Sep 21 14:43:09 2020[0;32m >> started[0m
Mon Sep 21 14:43:35 2020[0;32m >> done[0m (25.813s)
500000 read pairs processed; of these:
0 ( 0.00%) short read pairs filtered out after trimming by size control
0 ( 0.00%) empty read pairs filtered out after trimming by size control
500000 (100.00%) read pairs available; of these:
500000 (100.00%) untrimmed read pairs available after processing
log has been saved to "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2-trimmed.log".
Command completed. Elapsed time: 0:00:26. Running peak memory: 0.003GB.
PID: 9185; Command: skewer; Return code: 0; Memory used: 0.003GB
> `mv /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2-trimmed-pair1.fastq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1_trim.fastq` (9225)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.003GB.
PID: 9225; Command: mv; Return code: 0; Memory used: 0.001GB
> `mv /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2-trimmed-pair2.fastq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R2_trim.fastq` (9226)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.003GB.
PID: 9226; Command: mv; Return code: 0; Memory used: 0.0GB
Evaluating read trimming
> `Trimmed_reads` 1000000 PEPATAC _RES_
> `Trim_loss_rate` 0.0 PEPATAC _RES_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1_trim_fastqc.html`
> `fastqc --noextract --outdir /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastqc /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1_trim.fastq` (9231)
Started analysis of tutorial2_R1_trim.fastq
Approx 5% complete for tutorial2_R1_trim.fastq
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Approx 100% complete for tutorial2_R1_trim.fastq
Analysis complete for tutorial2_R1_trim.fastq
Command completed. Elapsed time: 0:00:07. Running peak memory: 0.173GB.
PID: 9231; Command: fastqc; Return code: 0; Memory used: 0.173GB
> `FastQC report r1` fastq/tutorial2_R1_trim_fastqc.html FastQC report r1 None PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R2_trim_fastqc.html`
> `fastqc --noextract --outdir /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastqc /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R2_trim.fastq` (9263)
Started analysis of tutorial2_R2_trim.fastq
Approx 5% complete for tutorial2_R2_trim.fastq
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Approx 15% complete for tutorial2_R2_trim.fastq
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Approx 95% complete for tutorial2_R2_trim.fastq
Approx 100% complete for tutorial2_R2_trim.fastq
Analysis complete for tutorial2_R2_trim.fastq
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.173GB.
PID: 9263; Command: fastqc; Return code: 0; Memory used: 0.171GB
> `FastQC report r2` fastq/tutorial2_R2_trim_fastqc.html FastQC report r2 None PEPATAC _OBJ_
### Prealignments (09-21 14:43:48) elapsed: 39.0 _TIME_
Prealignment assemblies: ['rCRSd', 'human_repeats']
### Map to rCRSd (09-21 14:43:48) elapsed: 0.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/rCRSd_bt2`
> `mkfifo /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/rCRSd_bt2` (9296)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.173GB.
PID: 9296; Command: mkfifo; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_bt_aln_summary.log`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R2.fq.gz`
> `perl /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/filter_paired_fq.pl /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/rCRSd_bt2 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1_trim.fastq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R2_trim.fastq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R1.fq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R2.fq` (9298)
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_bt_aln_summary.log`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R2.fq.gz`
> `(bowtie2 -p 4 -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 tutorial2 -U /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/fastq/tutorial2_R1_trim.fastq --un /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/rCRSd_bt2 > /dev/null) 2>/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_bt_aln_summary.log` (9299)
not gzipping output
Command completed. Elapsed time: 0:00:15. Running peak memory: 0.173GB.
PID: 9299; Command: bowtie2; Return code: 0; Memory used: 0.068GB
> `grep 'aligned exactly 1 time' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_bt_aln_summary.log | awk '{print $1}'`
> `Aligned_reads_rCRSd` 100556.0 PEPATAC _RES_
> `Alignment_rate_rCRSd` 10.06 PEPATAC _RES_
### Map to human_repeats (09-21 14:44:03) elapsed: 15.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/human_repeats_bt2`
> `mkfifo /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/human_repeats_bt2` (9350)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.173GB.
PID: 9350; Command: mkfifo; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_bt_aln_summary.log`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R2.fq.gz`
> `perl /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/filter_paired_fq.pl /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/human_repeats_bt2 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R1.fq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R2.fq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R1.fq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R2.fq` (9351)
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_bt_aln_summary.log`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R2.fq.gz`
> `(bowtie2 -p 4 -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 tutorial2 -U /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R1.fq --un /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/human_repeats_bt2 > /dev/null) 2>/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_bt_aln_summary.log` (9352)
not gzipping output
50278 reads skipped
0 reads lost
Command completed. Elapsed time: 0:00:16. Running peak memory: 0.173GB.
PID: 9352; Command: bowtie2; Return code: 0; Memory used: 0.072GB
> `grep 'aligned exactly 1 time' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_bt_aln_summary.log | awk '{print $1}'`
> `Aligned_reads_human_repeats` 19842.0 PEPATAC _RES_
> `Alignment_rate_human_repeats` 1.98 PEPATAC _RES_
### Compress all unmapped read files (09-21 14:44:19) elapsed: 16.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R1.fq.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R1.fq` (9421)
Command completed. Elapsed time: 0:00:08. Running peak memory: 0.173GB.
PID: 9421; Command: pigz; Return code: 0; Memory used: 0.003GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R2.fq.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_rCRSd_unmap_R2.fq` (9451)
9921 reads skipped
0 reads lost
Command completed. Elapsed time: 0:00:07. Running peak memory: 0.173GB.
PID: 9451; Command: pigz; Return code: 0; Memory used: 0.003GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R1.fq.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R1.fq` (9584)
Command completed. Elapsed time: 0:00:07. Running peak memory: 0.173GB.
PID: 9584; Command: pigz; Return code: 0; Memory used: 0.003GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R2.fq.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R2.fq` (9604)
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.173GB.
PID: 9604; Command: pigz; Return code: 0; Memory used: 0.003GB
### Map to genome (09-21 14:44:47) elapsed: 28.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam`
> `bowtie2 -p 4 --very-sensitive -X 2000 --rg-id tutorial2 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R1.fq.gz -2 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/prealignments/tutorial2_human_repeats_unmap_R2.fq.gz | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tmpn2p9e68e -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_temp.bam` (9620,9621,9622)
439801 reads; of these:
439801 (100.00%) were paired; of these:
43 (0.01%) aligned concordantly 0 times
403030 (91.64%) aligned concordantly exactly 1 time
36728 (8.35%) aligned concordantly >1 times
----
43 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
43 pairs aligned 0 times concordantly or discordantly; of these:
86 mates make up the pairs; of these:
65 (75.58%) aligned 0 times
6 (6.98%) aligned exactly 1 time
15 (17.44%) aligned >1 times
99.99% overall alignment rate
Command completed. Elapsed time: 0:06:12. Running peak memory: 3.545GB.
PID: 9621; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 9620; Command: bowtie2; Return code: 0; Memory used: 3.545GB
PID: 9622; Command: samtools; Return code: 0; Memory used: 0.221GB
> `samtools view -b -q 10 -@ 4 -U /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_fail_qc.bam -f 2 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_temp.bam > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam` (10972)
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.545GB.
PID: 10972; Command: samtools; Return code: 0; Memory used: 0.013GB
> `Mapped_reads` 879537 PEPATAC _RES_
> `QC_filtered_reads` 3707 PEPATAC _RES_
> `Aligned_reads` 875830 PEPATAC _RES_
> `Alignment_rate` 87.58 PEPATAC _RES_
> `Total_efficiency` 87.58 PEPATAC _RES_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam.bai`
> `samtools index /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_temp.bam` (11006)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.545GB.
PID: 11006; Command: samtools; Return code: 0; Memory used: 0.022GB
> `samtools index /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam` (11013)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 11013; Command: samtools; Return code: 0; Memory used: 0.016GB
Missing stat 'Mitochondrial_reads'
> `samtools idxstats /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_temp.bam | grep -we 'chrM' -we 'ChrM' -we 'ChrMT' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd'| cut -f 3`
> `Mitochondrial_reads` 30 PEPATAC _RES_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_noMT.bam`
> `samtools idxstats /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_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' > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/chr_sizes.bed` (11019,11020,11021,11022)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 11022; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 11019; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 11021; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 11020; Command: cut; Return code: 0; Memory used: 0.001GB
> `samtools view -L /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/chr_sizes.bed -b -@ 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_noMT.bam` (11024)
Command completed. Elapsed time: 0:00:11. Running peak memory: 3.545GB.
PID: 11024; Command: samtools; Return code: 0; Memory used: 0.015GB
> `mv /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_noMT.bam /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam` (11044)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 11044; Command: mv; Return code: 0; Memory used: 0.0GB
> `samtools index /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam` (11045)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 11045; Command: samtools; Return code: 0; Memory used: 0.015GB
### Calculate NRF, PBC1, and PBC2 (09-21 14:51:32) elapsed: 405.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_bamQC.tsv`
> `/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamQC.py -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam -c 4 -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_bamQC.tsv` (11050)
Registering input file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam'
Temporary files will be stored in: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tmp_tutorial2_sort_gvvztbpo'
Processing with 4 cores...
Merging 52 files into output file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_bamQC.tsv'
Command completed. Elapsed time: 0:00:11. Running peak memory: 3.545GB.
PID: 11050; Command: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamQC.py; Return code: 0; Memory used: 0.342GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_bamQC.tsv`
> `NRF` 1.0 PEPATAC _RES_
> `PBC1` 1.0 PEPATAC _RES_
> `PBC2` 437908.0 PEPATAC _RES_
Missing stat 'Unmapped_reads'
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_unmap.bam`
> `samtools view -b -@ 4 -f 12 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_temp.bam > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_unmap.bam` (11091)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.545GB.
PID: 11091; Command: samtools; Return code: 0; Memory used: 0.006GB
> `samtools view -c -f 4 -@ 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_temp.bam`
> `Unmapped_reads` 65 PEPATAC _RES_
### Remove duplicates and produce signal tracks (09-21 14:51:48) elapsed: 16.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam`
> `samtools sort -n -@ 1 -T /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tmpawp6jjsj /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam | samtools view -h - -@ 1 | samblaster -r --ignoreUnmated 2> /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_dedup_metrics_log.txt | samtools view -b - -@ 1 | samtools sort - -@ 1 -T /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tmpawp6jjsj -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam` (11110,11111,11112,11113,11114)
Command completed. Elapsed time: 0:00:35. Running peak memory: 3.545GB.
PID: 11110; Command: samtools; Return code: 0; Memory used: 0.242GB
PID: 11112; Command: samblaster; Return code: 0; Memory used: 0.005GB
PID: 11114; Command: samtools; Return code: 0; Memory used: 0.241GB
PID: 11111; Command: samtools; Return code: 0; Memory used: 0.003GB
PID: 11113; Command: samtools; Return code: 0; Memory used: 0.004GB
> `samtools index /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam` (11261)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 11261; Command: samtools; Return code: 0; Memory used: 0.015GB
> `grep 'Removed' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_dedup_metrics_log.txt | tr -s ' ' | cut -f 3 -d ' '`
> `Duplicate_reads` 0 PEPATAC _RES_
> `Dedup_aligned_reads` 875830.0 PEPATAC _RES_
> `Dedup_alignment_rate` 87.58 PEPATAC _RES_
> `Dedup_total_efficiency` 87.58 PEPATAC _RES_
Missing stat 'Read_length'
> `samtools stats /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-`
> `Read_length` 42 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 (09-21 14:52:31) elapsed: 43.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_preseq_out.txt`
> `preseq c_curve -v -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_preseq_out.txt -B /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam` (11359)
BAM_INPUT
TOTAL READS = 437908
COUNTS_SUM = 437908
DISTINCT READS = 436959
DISTINCT COUNTS = 3
MAX COUNT = 3
COUNTS OF 1 = 436025
OBSERVED COUNTS (4)
1 436025
2 919
3 15
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.545GB.
PID: 11359; Command: preseq; Return code: 0; Memory used: 0.005GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_preseq_yield.txt`
> `preseq lc_extrap -v -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_preseq_yield.txt -B /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam` (11371)
BAM_INPUT
TOTAL READS = 437908
DISTINCT READS = 436959
DISTINCT COUNTS = 3
MAX COUNT = 3
COUNTS OF 1 = 436025
MAX TERMS = 2
OBSERVED COUNTS (4)
1 436025
2 919
3 15
ERROR: max count before zero is les than min required count (4), sample not sufficiently deep or duplicates removed
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.545GB.
PID: 11371; Command: preseq; Return code: 1; Memory used: 0.005GB
Subprocess returned nonzero result. Check above output for details
ERROR: Subprocess returned nonzero result, but pipeline is continuing because nofail=True
Unable to calculate library complexity.
### Produce signal tracks (09-21 14:52:41) elapsed: 11.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_exact.bw`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_smooth.bw`
> `/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamSitesToWig.py -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -e /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_shift.bed -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_exact.bw -w /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_smooth.bw -m atac -p 2 --variable-step --scale 875830.0` (11379)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam'
Temporary files will be stored in: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tmp_tutorial2_sort_dedup_cuttrace_w8vq05f2'
Processing with 1 cores...
Reduce step (merge files)...
Merging 52 files into output file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_exact.bw'
Merging 52 files into output file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_smooth.bw'
Command completed. Elapsed time: 0:21:06. Running peak memory: 3.545GB.
PID: 11379; Command: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.495GB
### Calculate TSS enrichment (09-21 15:13:47) elapsed: 1266.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_TSS_enrichment.txt`
> `/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/pyTssEnrichment.py -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed -p ends -c 4 -z -v -s 6 -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_TSS_enrichment.txt` (15806)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.545GB.
PID: 15806; Command: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.431GB
Missing stat 'TSS_score'
> `TSS_score` 13.2 PEPATAC _RES_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_TSS_enrichment.pdf`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R tss -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_TSS_enrichment.txt` (15863)
Generating TSS plot with /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_TSS_enrichment.txt
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
TSS enrichment plot completed!
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.545GB.
PID: 15863; Command: Rscript; Return code: 0; Memory used: 0.239GB
> `TSS enrichment` QC_hg38/tutorial2_TSS_enrichment.pdf TSS enrichment QC_hg38/tutorial2_TSS_enrichment.png PEPATAC _OBJ_
### Plot fragment distribution (09-21 15:14:11) elapsed: 23.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_fragLenDistribution.pdf`
> `perl /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/fragment_length_dist.pl /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_fragLen.txt` (15892)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.545GB.
PID: 15892; Command: perl; Return code: 0; Memory used: 0.006GB
> `sort -n /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_fragLen.txt | uniq -c > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_fragCount.txt` (15970,15971)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 15971; Command: uniq; Return code: 0; Memory used: 0.002GB
PID: 15970; Command: sort; Return code: 0; Memory used: 0.018GB
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R frag -l /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_fragLen.txt -c /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_fragCount.txt -p /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_fragLenDistribution.pdf -t /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_fragLenDistribution.txt` (15977)
Fragment distribution plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.545GB.
PID: 15977; Command: Rscript; Return code: 0; Memory used: 0.243GB
> `Fragment distribution` QC_hg38/tutorial2_fragLenDistribution.pdf Fragment distribution QC_hg38/tutorial2_fragLenDistribution.png PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_annotations.bed`
> `ln -sf /project/shefflab/genomes/hg38/feat_annotation/default/hg38_annotations.bed.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_annotations.bed.gz` (15999)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 15999; Command: ln; Return code: 0; Memory used: 0.0GB
> `pigz -f -p 4 -d -c /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_annotations.bed.gz > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_annotations.bed` (16005)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16005; Command: pigz; Return code: 0; Memory used: 0.002GB
### Call peaks (09-21 15:14:24) elapsed: 13.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks.narrowPeak`
> `macs2 callpeak -t /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_shift.bed -f BED --outdir /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38 -n tutorial2 -g hs --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01` (16049)
INFO @ Mon, 21 Sep 2020 15:14:24:
# Command line: callpeak -t /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_shift.bed -f BED --outdir /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38 -n tutorial2 -g hs --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01
# ARGUMENTS LIST:
# name = tutorial2
# format = BED
# ChIP-seq file = ['/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_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, 21 Sep 2020 15:14:24: #1 read tag files...
INFO @ Mon, 21 Sep 2020 15:14:24: #1 read treatment tags...
INFO @ Mon, 21 Sep 2020 15:14:25: #1 tag size is determined as 50 bps
INFO @ Mon, 21 Sep 2020 15:14:25: #1 tag size = 50.0
INFO @ Mon, 21 Sep 2020 15:14:25: #1 total tags in treatment: 875816
INFO @ Mon, 21 Sep 2020 15:14:25: #1 finished!
INFO @ Mon, 21 Sep 2020 15:14:25: #2 Build Peak Model...
INFO @ Mon, 21 Sep 2020 15:14:25: #2 Skipped...
INFO @ Mon, 21 Sep 2020 15:14:25: #2 Use 150 as fragment length
INFO @ Mon, 21 Sep 2020 15:14:25: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Mon, 21 Sep 2020 15:14:25: #3 Call peaks...
INFO @ Mon, 21 Sep 2020 15:14:25: # local lambda is disabled!
INFO @ Mon, 21 Sep 2020 15:14:25: #3 !!!! DYNAMIC LAMBDA IS DISABLED !!!!
INFO @ Mon, 21 Sep 2020 15:14:25: #3 Going to call summits inside each peak ...
INFO @ Mon, 21 Sep 2020 15:14:25: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Mon, 21 Sep 2020 15:14:25: #3 Pre-compute pvalue-qvalue table...
INFO @ Mon, 21 Sep 2020 15:14:26: #3 Call peaks for each chromosome...
INFO @ Mon, 21 Sep 2020 15:18:25: #4 Write output xls file... /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks.xls
INFO @ Mon, 21 Sep 2020 15:18:28: #4 Write peak in narrowPeak format file... /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks.narrowPeak
INFO @ Mon, 21 Sep 2020 15:18:29: #4 Write summits bed file... /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_summits.bed
INFO @ Mon, 21 Sep 2020 15:18:30: Done!
Command completed. Elapsed time: 0:04:07. Running peak memory: 3.545GB.
PID: 16049; Command: macs2; Return code: 0; Memory used: 0.118GB
> `Peak_count` 534448 PEPATAC _RES_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_shift.bed.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_shift.bed > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38_exact/tutorial2_shift.bed.gz` (16744)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 16744; Command: pigz; Return code: 0; Memory used: 0.005GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_fixedWidth.narrowPeak`
> `awk -v OFS=' ' '{$2 = int(($3 - $2)/2 + $2 - 250); $3 = int($2 + 500); print}' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks.narrowPeak > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_fixedWidth.narrowPeak` (16755)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 16755; Command: awk; Return code: 0; Memory used: 0.007GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_normalized.narrowPeak`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R reduce -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_fixedWidth.narrowPeak -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes --normalize` (16758)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.545GB.
PID: 16758; Command: Rscript; Return code: 0; Memory used: 0.584GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_blacklist.bed`
> `ln -sf /project/shefflab/genomes/hg38/blacklist/default/hg38_blacklist.bed.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_blacklist.bed.gz` (16795)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16795; Command: ln; Return code: 0; Memory used: 0.0GB
> `pigz -f -p 4 -d -c /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_blacklist.bed.gz > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_blacklist.bed` (16796)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16796; Command: pigz; Return code: 0; Memory used: 0.002GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_rmBlacklist.narrowPeak`
> `bedtools intersect -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_normalized.narrowPeak -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_blacklist.bed -v > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_rmBlacklist.narrowPeak` (16801)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 16801; Command: bedtools; Return code: 0; Memory used: 0.004GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/blacklist.flag`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R reduce -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_rmBlacklist.narrowPeak -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes` (16805)
Command completed. Elapsed time: 0:00:13. Running peak memory: 3.545GB.
PID: 16805; Command: Rscript; Return code: 0; Memory used: 0.226GB
> `touch /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/blacklist.flag` (16844)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16844; Command: touch; Return code: 0; Memory used: 0.0GB
### Calculate fraction of reads in peaks (FRiP) (09-21 15:19:04) elapsed: 281.0 _TIME_
Missing stat 'FRiP'
> `samtools view -@ 4 -c -L /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_normalized.narrowPeak /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam`
875830 804029
> `FRiP` 0.92 PEPATAC _RES_
### Calculate peak coverage (09-21 15:19:06) elapsed: 2.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt`
> `samtools view -H /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam | grep 'SN:' | awk -F':' '{print $2,$3}' | awk -F' ' -v OFS=' ' '{print $1,$3}' > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt` (16853,16854,16855,16856)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16854; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 16856; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 16853; Command: samtools; Return code: 0; Memory used: 0.003GB
PID: 16855; Command: awk; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_sort.bed`
> `cut -f 1-3 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_normalized.narrowPeak > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks.bed` (16858)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16858; Command: cut; Return code: 0; Memory used: 0.002GB
> `samtools view -H /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam | grep 'SN:' | awk -F':' '{print $2,$3}' | awk -F' ' -v OFS=' ' '{print $1,$3}' > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt` (16860,16861,16862,16863)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16860; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 16862; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 16861; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 16863; Command: awk; Return code: 0; Memory used: 0.0GB
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_keep.txt` (16865)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16865; Command: cut; Return code: 0; Memory used: 0.002GB
> `bedtools sort -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks.bed -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_sort.bed` (16867)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 16867; Command: bedtools; Return code: 0; Memory used: 0.006GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/coverage.flag`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt | uniq > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_coverage.bed` (16870,16871)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.545GB.
PID: 16870; Command: bedtools; Return code: 0; Memory used: 0.011GB
PID: 16871; Command: uniq; Return code: 0; Memory used: 0.002GB
> `awk 'BEGIN{OFS="\t";} NR==FNR{sum += $5; next}{if (sum <= 0){sum = 1} print $1, $2, $3, $4, $5, $6, $7, ($5/sum*1000000)}' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_coverage.bed > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_norm_peaks_coverage.bed` (16894)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 16894; Command: awk; Return code: 0; Memory used: 0.011GB
> `mv /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_norm_peaks_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_coverage.bed` (16896)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16896; Command: mv; Return code: 0; Memory used: 0.0GB
> `touch /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/coverage.flag` (16897)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16897; Command: touch; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_coverage.bed.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_coverage.bed > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_coverage.bed.gz` (16901)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 16901; Command: pigz; Return code: 0; Memory used: 0.005GB
### # Produce bigBed formatted narrowPeak file (09-21 15:19:13) elapsed: 7.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/bigNarrowPeak.as`
> `echo 'table bigNarrowPeak
"BED6+4 Peaks of signal enrichment based on pooled, normalized (interpreted) data."
(
string chrom; "Reference sequence chromosome or scaffold"
uint chromStart; "Start position in chromosome"
uint chromEnd; "End position in chromosome"
string name; "Name given to a region (preferably unique). Use . if no name is assigned"
uint score; "Indicates how dark the peak will be displayed in the browser (0-1000) "
char[1] strand; "+ or - or . for unknown"
float signalValue; "Measurement of average enrichment for the region"
float pValue; "Statistical significance of signal value (-log10). Set to -1 if not used."
float qValue; "Statistical significance with multiple-test correction applied (FDR -log10). Set to -1 if not used."
int peak; "Point-source called for this peak; 0-based offset from chromStart. Set to -1 if no point-source called."
)' > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/bigNarrowPeak.as` (16921)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 16921; Command: echo; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks.bigBed`
> `bedToBigBed -as=/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/bigNarrowPeak.as -type=bed6+4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tmpdppqd4sz /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks.bigBed` (16922)
pass1 - making usageList (52 chroms): 69 millis
pass2 - checking and writing primary data (352486 records, 10 fields): 890 millis
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 16922; Command: bedToBigBed; Return code: 0; Memory used: 0.004GB
### Annotate peaks (09-21 15:19:17) elapsed: 4.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_peak_chromosome_distribution.pdf`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R anno -p chromosome -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_normalized.narrowPeak -f /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_annotations.bed -g hg38 -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_peak_chromosome_distribution.pdf` (16924)
chromosome distribution plot completed!
Command completed. Elapsed time: 0:00:35. Running peak memory: 3.545GB.
PID: 16924; Command: Rscript; Return code: 0; Memory used: 0.53GB
> `Peak chromosome distribution` QC_hg38/tutorial2_peak_chromosome_distribution.pdf Peak chromosome distribution QC_hg38/tutorial2_peak_chromosome_distribution.png PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_peak_TSS_distribution.pdf`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R anno -p tss -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_normalized.narrowPeak -f /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_annotations.bed -g hg38 -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_peak_TSS_distribution.pdf` (16989)
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
tss distribution plot completed!
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.545GB.
PID: 16989; Command: Rscript; Return code: 0; Memory used: 0.528GB
> `TSS distance distribution` QC_hg38/tutorial2_peak_TSS_distribution.pdf TSS distance distribution QC_hg38/tutorial2_peak_TSS_distribution.png PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_peak_genomic_distribution.pdf`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R anno -p genomic -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/tutorial2_peaks_normalized.narrowPeak -f /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_annotations.bed -g hg38 -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_peak_genomic_distribution.pdf` (17224)
genomic distribution plot completed!
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.545GB.
PID: 17224; Command: Rscript; Return code: 0; Memory used: 0.653GB
> `Peak partition distribution` QC_hg38/tutorial2_peak_genomic_distribution.pdf Peak partition distribution QC_hg38/tutorial2_peak_genomic_distribution.png PEPATAC _OBJ_
### Calculate read coverage (09-21 15:20:23) elapsed: 65.0 _TIME_
> `cut -f 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_annotations.bed | sort -u`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/3' UTR`
> `awk -F' ' '{print>"/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/"$4}' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/raw/hg38_annotations.bed` (17271)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 17271; Command: awk; Return code: 0; Memory used: 0.005GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/3_UTR`
> `mv "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/3' UTR" "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/3_UTR"` (17274)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 17274; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/3_UTR_sort.bed` (17275,17276,17277,17278)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 17275; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 17277; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 17276; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 17278; Command: bedtools; Return code: 0; Memory used: 0.036GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_3_UTR_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/3_UTR_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_3_UTR_coverage.bed` (17281)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 17281; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/5' UTR`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/5_UTR`
> `mv "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/5' UTR" "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/5_UTR"` (17285)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 17285; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/5_UTR_sort.bed` (17286,17287,17288,17289)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 17286; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 17287; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 17289; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 17288; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_5_UTR_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/5_UTR_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_5_UTR_coverage.bed` (17292)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 17292; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Enhancer`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Enhancer_sort.bed` (17296,17297,17298,17299)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 17296; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 17298; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 17297; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 17299; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Enhancer_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Enhancer_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Enhancer_coverage.bed` (17305)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 17305; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Exon`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Exon_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Exon_sort.bed` (17310,17311,17312,17313)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.545GB.
PID: 17310; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 17311; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 17313; Command: bedtools; Return code: 0; Memory used: 0.167GB
PID: 17312; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Exon_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Exon_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Exon_coverage.bed` (17320)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.545GB.
PID: 17320; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Intron`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Intron_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Intron_sort.bed` (17325,17326,17327,17328)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 17325; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 17328; Command: bedtools; Return code: 0; Memory used: 0.076GB
PID: 17326; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 17327; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Intron_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Intron_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Intron_coverage.bed` (17332)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.545GB.
PID: 17332; Command: bedtools; Return code: 0; Memory used: 0.015GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter_sort.bed` (17340,17341,17342,17343)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.545GB.
PID: 17340; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 17341; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 17343; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 17342; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Promoter_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Promoter_coverage.bed` (17346)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 17346; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter Flanking Region`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter_Flanking_Region`
> `mv "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter Flanking Region" "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter_Flanking_Region"` (17351)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.545GB.
PID: 17351; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter_Flanking_Region_sort.bed` (17352,17353,17354,17355)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 17352; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 17354; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 17353; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 17355; Command: bedtools; Return code: 0; Memory used: 0.05GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Promoter_Flanking_Region_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/Promoter_Flanking_Region_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Promoter_Flanking_Region_coverage.bed` (17359)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.545GB.
PID: 17359; Command: bedtools; Return code: 0; Memory used: 0.009GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (09-21 15:20:52) elapsed: 30.0 _TIME_
> `samtools view -@ 4 -q 10 -c -F4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort_dedup.bam`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_cFRiF.pdf`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R frif -s tutorial2 -z 3099922541 -n 875816 -y cfrif --reads -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_cFRiF.pdf --bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_3_UTR_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_5_UTR_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Enhancer_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Exon_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Intron_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Promoter_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Promoter_Flanking_Region_coverage.bed` (17379)
FRiF plot completed!
Command completed. Elapsed time: 0:00:38. Running peak memory: 3.545GB.
PID: 17379; Command: Rscript; Return code: 0; Memory used: 0.584GB
> `cFRiF` QC_hg38/tutorial2_cFRiF.pdf cFRiF QC_hg38/tutorial2_cFRiF.png PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_FRiF.pdf`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R frif -s tutorial2 -z 3099922541 -n 875816 -y frif --reads -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_FRiF.pdf --bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_3_UTR_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_5_UTR_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Enhancer_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Exon_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Intron_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Promoter_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_Promoter_Flanking_Region_coverage.bed` (17452)
FRiF plot completed!
Command completed. Elapsed time: 0:00:35. Running peak memory: 3.545GB.
PID: 17452; Command: Rscript; Return code: 0; Memory used: 0.55GB
> `FRiF` QC_hg38/tutorial2_FRiF.pdf FRiF QC_hg38/tutorial2_FRiF.png PEPATAC _OBJ_
Starting cleanup: 39 files; 3 conditional files for cleanup
Cleaning up flagged intermediate files. . .
Cleaning up conditional list. . .
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:39:02
* Total elapsed time (all runs): 0:53:17
* Peak memory (this run): 3.5449 GB
* Pipeline completed time: 2020-09-21 15:22:06