### Pipeline run code and environment:
* Command: `/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/pipelines/pepatac.py --sample-name tutorial1 --genome hg38 --input /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial1_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/tutorial1_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/tutorial1/
* Pipeline started at: (09-21 14:04:14) elapsed: 0.0 _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/tutorial1_r1.fastq.gz']`
* `input2`: `['/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial1_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`: `tutorial1`
* `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/tutorial1_r1.fastq.gz
Local input file: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial1_r2.fastq.gz
> `File_mb` 27 2 _RES_
> `Read_type` paired PEPATAC _RES_
> `Genome` hg38 PEPATAC _RES_
### Merge/link and fastq conversion: (09-21 14:04:14) elapsed: 1.0 _TIME_
Number of input file sets: 2
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/tutorial1_R1.fastq.gz`
> `ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial1_r1.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/tutorial1_R1.fastq.gz` (32206)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 32206; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/tutorial1_R1.fastq.gz'
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/tutorial1_R2.fastq.gz`
> `ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/data/tutorial1_r2.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/tutorial1_R2.fastq.gz` (32207)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 32207; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/tutorial1_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/tutorial1/raw/tutorial1_R1.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R1.fastq.gz', 'ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/tutorial1_R2.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R2.fastq.gz']
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R1.fastq.gz`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R2.fastq.gz`
> `ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/tutorial1_R1.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R1.fastq.gz` (32208)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 32208; Command: ln; Return code: 0; Memory used: 0.0GB
> `ln -sf /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/tutorial1_R2.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R2.fastq.gz` (32209)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 32209; Command: ln; Return code: 0; Memory used: 0.0GB
> `Raw_reads` 1000000 PEPATAC _RES_
> `Fastq_reads` 1000000 PEPATAC _RES_
### Adapter trimming: (09-21 14:04:16) elapsed: 2.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_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/tutorial1/fastq/tutorial1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R1.fastq.gz /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R2.fastq.gz` (32245)
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 14:04:16 2020[0;32m >> started[0m
Mon Sep 21 14:04:41 2020[0;32m >> done[0m (24.928s)
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/tutorial1/fastq/tutorial1-trimmed.log".
Command completed. Elapsed time: 0:00:25. Running peak memory: 0.003GB.
PID: 32245; Command: skewer; Return code: 0; Memory used: 0.003GB
> `mv /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1-trimmed-pair1.fastq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R1_trim.fastq` (32280)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.003GB.
PID: 32280; Command: mv; Return code: 0; Memory used: 0.0GB
> `mv /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1-trimmed-pair2.fastq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R2_trim.fastq` (32281)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.003GB.
PID: 32281; 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/tutorial1/fastq/tutorial1_R1_trim_fastqc.html`
> `fastqc --noextract --outdir /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastqc /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R1_trim.fastq` (32286)
Started analysis of tutorial1_R1_trim.fastq
Approx 5% complete for tutorial1_R1_trim.fastq
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Approx 100% complete for tutorial1_R1_trim.fastq
Analysis complete for tutorial1_R1_trim.fastq
Command completed. Elapsed time: 0:00:07. Running peak memory: 0.164GB.
PID: 32286; Command: fastqc; Return code: 0; Memory used: 0.164GB
> `FastQC report r1` fastq/tutorial1_R1_trim_fastqc.html FastQC report r1 None PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R2_trim_fastqc.html`
> `fastqc --noextract --outdir /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastqc /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R2_trim.fastq` (32325)
Started analysis of tutorial1_R2_trim.fastq
Approx 5% complete for tutorial1_R2_trim.fastq
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Approx 90% complete for tutorial1_R2_trim.fastq
Approx 95% complete for tutorial1_R2_trim.fastq
Approx 100% complete for tutorial1_R2_trim.fastq
Analysis complete for tutorial1_R2_trim.fastq
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.172GB.
PID: 32325; Command: fastqc; Return code: 0; Memory used: 0.172GB
> `FastQC report r2` fastq/tutorial1_R2_trim_fastqc.html FastQC report r2 None PEPATAC _OBJ_
### Prealignments (09-21 14:04:55) elapsed: 39.0 _TIME_
Prealignment assemblies: ['rCRSd', 'human_repeats']
### Map to rCRSd (09-21 14:04:55) elapsed: 0.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/rCRSd_bt2`
> `mkfifo /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/rCRSd_bt2` (32361)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.172GB.
PID: 32361; Command: mkfifo; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_bt_aln_summary.log`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_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/tutorial1/prealignments/rCRSd_bt2 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R1_trim.fastq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R2_trim.fastq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_unmap_R1.fq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_unmap_R2.fq` (32362)
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_bt_aln_summary.log`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_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 tutorial1 -U /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/fastq/tutorial1_R1_trim.fastq --un /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/rCRSd_bt2 > /dev/null) 2>/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_bt_aln_summary.log` (32363)
not gzipping output
Command completed. Elapsed time: 0:00:14. Running peak memory: 0.172GB.
PID: 32363; Command: bowtie2; Return code: 0; Memory used: 0.068GB
> `grep 'aligned exactly 1 time' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_bt_aln_summary.log | awk '{print $1}'`
> `Aligned_reads_rCRSd` 99360.0 PEPATAC _RES_
> `Alignment_rate_rCRSd` 9.94 PEPATAC _RES_
### Map to human_repeats (09-21 14:05:09) elapsed: 15.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/human_repeats_bt2`
> `mkfifo /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/human_repeats_bt2` (32545)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.172GB.
PID: 32545; Command: mkfifo; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_bt_aln_summary.log`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_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/tutorial1/prealignments/human_repeats_bt2 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_unmap_R1.fq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_unmap_R2.fq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_unmap_R1.fq /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_unmap_R2.fq` (32546)
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_bt_aln_summary.log`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_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 tutorial1 -U /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_unmap_R1.fq --un /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/human_repeats_bt2 > /dev/null) 2>/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_bt_aln_summary.log` (32547)
not gzipping output
49680 reads skipped
0 reads lost
Command completed. Elapsed time: 0:00:16. Running peak memory: 0.172GB.
PID: 32547; Command: bowtie2; Return code: 0; Memory used: 0.072GB
> `grep 'aligned exactly 1 time' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_bt_aln_summary.log | awk '{print $1}'`
> `Aligned_reads_human_repeats` 20102.0 PEPATAC _RES_
> `Alignment_rate_human_repeats` 2.01 PEPATAC _RES_
### Compress all unmapped read files (09-21 14:05:25) elapsed: 16.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_unmap_R1.fq.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_unmap_R1.fq` (32576)
Command completed. Elapsed time: 0:00:08. Running peak memory: 0.172GB.
PID: 32576; Command: pigz; Return code: 0; Memory used: 0.003GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_unmap_R2.fq.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_rCRSd_unmap_R2.fq` (32592)
10051 reads skipped
0 reads lost
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.172GB.
PID: 32592; Command: pigz; Return code: 0; Memory used: 0.003GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_unmap_R1.fq.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_unmap_R1.fq` (32604)
Command completed. Elapsed time: 0:00:08. Running peak memory: 0.172GB.
PID: 32604; Command: pigz; Return code: 0; Memory used: 0.003GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_unmap_R2.fq.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_unmap_R2.fq` (32620)
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.172GB.
PID: 32620; Command: pigz; Return code: 0; Memory used: 0.003GB
### Map to genome (09-21 14:05:53) elapsed: 28.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam`
> `bowtie2 -p 4 --very-sensitive -X 2000 --rg-id tutorial1 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_unmap_R1.fq.gz -2 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/prealignments/tutorial1_human_repeats_unmap_R2.fq.gz | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tmpuh0mv4hp -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_temp.bam` (32635,32636,32637)
440269 reads; of these:
440269 (100.00%) were paired; of these:
40 (0.01%) aligned concordantly 0 times
403728 (91.70%) aligned concordantly exactly 1 time
36501 (8.29%) aligned concordantly >1 times
----
40 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
40 pairs aligned 0 times concordantly or discordantly; of these:
80 mates make up the pairs; of these:
59 (73.75%) aligned 0 times
7 (8.75%) aligned exactly 1 time
14 (17.50%) aligned >1 times
99.99% overall alignment rate
Command completed. Elapsed time: 0:06:36. Running peak memory: 3.544GB.
PID: 32637; Command: samtools; Return code: 0; Memory used: 0.218GB
PID: 32635; Command: bowtie2; Return code: 0; Memory used: 3.544GB
PID: 32636; Command: samtools; Return code: 0; Memory used: 0.004GB
> `samtools view -b -q 10 -@ 4 -U /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_fail_qc.bam -f 2 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_temp.bam > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam` (1500)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.544GB.
PID: 1500; Command: samtools; Return code: 0; Memory used: 0.013GB
> `Mapped_reads` 880479 PEPATAC _RES_
> `QC_filtered_reads` 3539 PEPATAC _RES_
> `Aligned_reads` 876940 PEPATAC _RES_
> `Alignment_rate` 87.69 PEPATAC _RES_
> `Total_efficiency` 87.69 PEPATAC _RES_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam.bai`
> `samtools index /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_temp.bam` (1546)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 1546; Command: samtools; Return code: 0; Memory used: 0.016GB
> `samtools index /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam` (1551)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 1551; Command: samtools; Return code: 0; Memory used: 0.017GB
Missing stat 'Mitochondrial_reads'
> `samtools idxstats /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_temp.bam | grep -we 'chrM' -we 'ChrM' -we 'ChrMT' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd'| cut -f 3`
> `Mitochondrial_reads` 18 PEPATAC _RES_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_noMT.bam`
> `samtools idxstats /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_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/tutorial1/aligned_hg38/chr_sizes.bed` (1559,1560,1561,1562)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 1562; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 1559; Command: samtools; Return code: 0; Memory used: 0.005GB
PID: 1561; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 1560; Command: cut; Return code: 0; Memory used: 0.001GB
> `samtools view -L /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/chr_sizes.bed -b -@ 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_noMT.bam` (1564)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.544GB.
PID: 1564; Command: samtools; Return code: 0; Memory used: 0.015GB
> `mv /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_noMT.bam /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam` (1584)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 1584; Command: mv; Return code: 0; Memory used: 0.0GB
> `samtools index /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam` (1585)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 1585; Command: samtools; Return code: 0; Memory used: 0.017GB
### Calculate NRF, PBC1, and PBC2 (09-21 14:12:53) elapsed: 420.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_bamQC.tsv`
> `/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamQC.py -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam -c 4 -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_bamQC.tsv` (1589)
Registering input file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam'
Temporary files will be stored in: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tmp_tutorial1_sort_3nh89p4l'
Processing with 4 cores...
Merging 53 files into output file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_bamQC.tsv'
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.544GB.
PID: 1589; Command: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamQC.py; Return code: 0; Memory used: 0.354GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_bamQC.tsv`
> `NRF` 1.0 PEPATAC _RES_
> `PBC1` 1.0 PEPATAC _RES_
> `PBC2` 438465.0 PEPATAC _RES_
Missing stat 'Unmapped_reads'
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_unmap.bam`
> `samtools view -b -@ 4 -f 12 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_temp.bam > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_unmap.bam` (1634)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 1634; Command: samtools; Return code: 0; Memory used: 0.005GB
> `samtools view -c -f 4 -@ 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_temp.bam`
> `Unmapped_reads` 59 PEPATAC _RES_
### Remove duplicates and produce signal tracks (09-21 14:13:04) elapsed: 11.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam`
> `samtools sort -n -@ 1 -T /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tmpqxlr3h_m /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam | samtools view -h - -@ 1 | samblaster -r --ignoreUnmated 2> /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_dedup_metrics_log.txt | samtools view -b - -@ 1 | samtools sort - -@ 1 -T /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tmpqxlr3h_m -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam` (1655,1656,1657,1658,1659)
Command completed. Elapsed time: 0:00:30. Running peak memory: 3.544GB.
PID: 1655; Command: samtools; Return code: 0; Memory used: 0.242GB
PID: 1657; Command: samblaster; Return code: 0; Memory used: 0.005GB
PID: 1659; Command: samtools; Return code: 0; Memory used: 0.221GB
PID: 1656; Command: samtools; Return code: 0; Memory used: 0.003GB
PID: 1658; Command: samtools; Return code: 0; Memory used: 0.004GB
> `samtools index /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam` (1706)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 1706; Command: samtools; Return code: 0; Memory used: 0.017GB
> `grep 'Removed' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_dedup_metrics_log.txt | tr -s ' ' | cut -f 3 -d ' '`
> `Duplicate_reads` 0 PEPATAC _RES_
> `Dedup_aligned_reads` 876940.0 PEPATAC _RES_
> `Dedup_alignment_rate` 87.69 PEPATAC _RES_
> `Dedup_total_efficiency` 87.69 PEPATAC _RES_
Missing stat 'Read_length'
> `samtools stats /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_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 14:13:40) elapsed: 36.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_out.txt`
> `preseq c_curve -v -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_out.txt -B /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam` (1731)
BAM_INPUT
TOTAL READS = 438466
COUNTS_SUM = 438466
DISTINCT READS = 437508
DISTINCT COUNTS = 4
MAX COUNT = 4
COUNTS OF 1 = 436566
OBSERVED COUNTS (5)
1 436566
2 927
3 14
4 1
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.544GB.
PID: 1731; Command: preseq; Return code: 0; Memory used: 0.005GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_yield.txt`
> `preseq lc_extrap -v -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_yield.txt -B /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam` (1740)
BAM_INPUT
TOTAL READS = 438466
DISTINCT READS = 437508
DISTINCT COUNTS = 4
MAX COUNT = 4
COUNTS OF 1 = 436566
MAX TERMS = 4
OBSERVED COUNTS (5)
1 436566
2 927
3 14
4 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
._.._._.._..__..._._.___._.___...__.___..__._.__...___...__.....__._........___..__._.__.._._....__.__..._.___..._._._...__.._.__..__.._..._._..__..........._.._..__._....
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.544GB.
PID: 1740; Command: preseq; Return code: 0; Memory used: 0.005GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_counts.txt`
> `echo '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_yield.txt '$(samtools view -c -F 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort.bam)' '$(samtools view -c -F 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam) > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_counts.txt` (1746)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.544GB.
PID: 1746; Command: echo; Return code: 0; Memory used: 0.005GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_plot.pdf`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_plot.png`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R preseq -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_yield.txt -r /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_counts.txt -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_plot` (1755)
INFO: Found real counts for tutorial1 - Total (M): 0.87693 Unique (M): 0.87693
Library complexity plot completed!
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.544GB.
PID: 1755; Command: Rscript; Return code: 0; Memory used: 0.212GB
> `Library complexity` QC_hg38/tutorial1_preseq_plot.pdf Library complexity QC_hg38/tutorial1_preseq_plot.png PEPATAC _OBJ_
Missing stat 'Frac_exp_unique_at_10M'
> `grep -w '^10000000' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_preseq_yield.txt | awk '{print $2}'`
> `Frac_exp_unique_at_10M` 0.9572 PEPATAC _RES_
### Produce signal tracks (09-21 14:14:00) elapsed: 20.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_exact.bw`,`/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_smooth.bw`
> `/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamSitesToWig.py -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -e /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_shift.bed -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_exact.bw -w /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_smooth.bw -m atac -p 2 --variable-step --scale 876940.0` (1783)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam'
Temporary files will be stored in: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tmp_tutorial1_sort_dedup_cuttrace_6u3kypgq'
Processing with 1 cores...
Reduce step (merge files)...
Merging 53 files into output file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_exact.bw'
Merging 53 files into output file: '/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_smooth.bw'
Command completed. Elapsed time: 0:20:32. Running peak memory: 3.544GB.
PID: 1783; Command: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/bamSitesToWig.py; Return code: 0; Memory used: 1.859GB
### Calculate TSS enrichment (09-21 14:34:32) elapsed: 1232.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_TSS_enrichment.txt`
> `/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/pyTssEnrichment.py -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_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/tutorial1/QC_hg38/tutorial1_TSS_enrichment.txt` (6822)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.544GB.
PID: 6822; Command: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.404GB
Missing stat 'TSS_score'
> `TSS_score` 14.3 PEPATAC _RES_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_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/tutorial1/QC_hg38/tutorial1_TSS_enrichment.txt` (6862)
Generating TSS plot with /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_TSS_enrichment.txt
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
TSS enrichment plot completed!
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.544GB.
PID: 6862; Command: Rscript; Return code: 0; Memory used: 0.213GB
> `TSS enrichment` QC_hg38/tutorial1_TSS_enrichment.pdf TSS enrichment QC_hg38/tutorial1_TSS_enrichment.png PEPATAC _OBJ_
### Plot fragment distribution (09-21 14:34:56) elapsed: 24.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_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/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_fragLen.txt` (6894)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.544GB.
PID: 6894; Command: perl; Return code: 0; Memory used: 0.006GB
> `sort -n /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_fragLen.txt | uniq -c > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_fragCount.txt` (6899,6900)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 6899; Command: sort; Return code: 0; Memory used: 0.018GB
PID: 6900; Command: uniq; Return code: 0; Memory used: 0.002GB
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R frag -l /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_fragLen.txt -c /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_fragCount.txt -p /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_fragLenDistribution.pdf -t /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_fragLenDistribution.txt` (7061)
Fragment distribution plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.544GB.
PID: 7061; Command: Rscript; Return code: 0; Memory used: 0.213GB
> `Fragment distribution` QC_hg38/tutorial1_fragLenDistribution.pdf Fragment distribution QC_hg38/tutorial1_fragLenDistribution.png PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/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/tutorial1/raw/hg38_annotations.bed.gz` (7081)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 7081; Command: ln; Return code: 0; Memory used: 0.001GB
> `pigz -f -p 4 -d -c /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_annotations.bed.gz > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_annotations.bed` (7082)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 7082; Command: pigz; Return code: 0; Memory used: 0.002GB
### Call peaks (09-21 14:35:08) elapsed: 12.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks.narrowPeak`
> `macs2 callpeak -t /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_shift.bed -f BED --outdir /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38 -n tutorial1 -g hs --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01` (7088)
INFO @ Mon, 21 Sep 2020 14:35:09:
# Command line: callpeak -t /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_shift.bed -f BED --outdir /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38 -n tutorial1 -g hs --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01
# ARGUMENTS LIST:
# name = tutorial1
# format = BED
# ChIP-seq file = ['/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_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 14:35:09: #1 read tag files...
INFO @ Mon, 21 Sep 2020 14:35:09: #1 read treatment tags...
INFO @ Mon, 21 Sep 2020 14:35:10: #1 tag size is determined as 50 bps
INFO @ Mon, 21 Sep 2020 14:35:10: #1 tag size = 50.0
INFO @ Mon, 21 Sep 2020 14:35:10: #1 total tags in treatment: 876930
INFO @ Mon, 21 Sep 2020 14:35:10: #1 finished!
INFO @ Mon, 21 Sep 2020 14:35:10: #2 Build Peak Model...
INFO @ Mon, 21 Sep 2020 14:35:10: #2 Skipped...
INFO @ Mon, 21 Sep 2020 14:35:10: #2 Use 150 as fragment length
INFO @ Mon, 21 Sep 2020 14:35:10: #2 Sequencing ends will be shifted towards 5' by 75 bp(s)
INFO @ Mon, 21 Sep 2020 14:35:10: #3 Call peaks...
INFO @ Mon, 21 Sep 2020 14:35:10: # local lambda is disabled!
INFO @ Mon, 21 Sep 2020 14:35:10: #3 !!!! DYNAMIC LAMBDA IS DISABLED !!!!
INFO @ Mon, 21 Sep 2020 14:35:10: #3 Going to call summits inside each peak ...
INFO @ Mon, 21 Sep 2020 14:35:10: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ...
INFO @ Mon, 21 Sep 2020 14:35:10: #3 Pre-compute pvalue-qvalue table...
INFO @ Mon, 21 Sep 2020 14:35:11: #3 Call peaks for each chromosome...
INFO @ Mon, 21 Sep 2020 14:39:08: #4 Write output xls file... /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks.xls
INFO @ Mon, 21 Sep 2020 14:39:10: #4 Write peak in narrowPeak format file... /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks.narrowPeak
INFO @ Mon, 21 Sep 2020 14:39:11: #4 Write summits bed file... /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_summits.bed
INFO @ Mon, 21 Sep 2020 14:39:12: Done!
Command completed. Elapsed time: 0:04:04. Running peak memory: 3.544GB.
PID: 7088; Command: macs2; Return code: 0; Memory used: 0.12GB
> `Peak_count` 535285 PEPATAC _RES_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_shift.bed.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_shift.bed > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38_exact/tutorial1_shift.bed.gz` (8016)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.544GB.
PID: 8016; Command: pigz; Return code: 0; Memory used: 0.005GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_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/tutorial1/peak_calling_hg38/tutorial1_peaks.narrowPeak > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_fixedWidth.narrowPeak` (8026)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8026; Command: awk; Return code: 0; Memory used: 0.007GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_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/tutorial1/peak_calling_hg38/tutorial1_peaks_fixedWidth.narrowPeak -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes --normalize` (8028)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.544GB.
PID: 8028; Command: Rscript; Return code: 0; Memory used: 0.671GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/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/tutorial1/raw/hg38_blacklist.bed.gz` (8067)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8067; Command: ln; Return code: 0; Memory used: 0.0GB
> `pigz -f -p 4 -d -c /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_blacklist.bed.gz > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_blacklist.bed` (8068)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8068; Command: pigz; Return code: 0; Memory used: 0.002GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_rmBlacklist.narrowPeak`
> `bedtools intersect -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_normalized.narrowPeak -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_blacklist.bed -v > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_rmBlacklist.narrowPeak` (8073)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8073; Command: bedtools; Return code: 0; Memory used: 0.004GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/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/tutorial1/peak_calling_hg38/tutorial1_peaks_rmBlacklist.narrowPeak -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes` (8075)
Command completed. Elapsed time: 0:00:13. Running peak memory: 3.544GB.
PID: 8075; Command: Rscript; Return code: 0; Memory used: 0.296GB
> `touch /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/blacklist.flag` (8112)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8112; Command: touch; Return code: 0; Memory used: 0.001GB
### Calculate fraction of reads in peaks (FRiP) (09-21 14:39:44) elapsed: 275.0 _TIME_
Missing stat 'FRiP'
> `samtools view -@ 4 -c -L /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_normalized.narrowPeak /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam`
876940 804980
> `FRiP` 0.92 PEPATAC _RES_
### Calculate peak coverage (09-21 14:39:46) elapsed: 2.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt`
> `samtools view -H /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_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/tutorial1/peak_calling_hg38/chr_order.txt` (8123,8124,8125,8126)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8123; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 8125; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 8124; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 8126; Command: awk; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_sort.bed`
> `cut -f 1-3 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_normalized.narrowPeak > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks.bed` (8129)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8129; Command: cut; Return code: 0; Memory used: 0.002GB
> `samtools view -H /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_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/tutorial1/peak_calling_hg38/chr_order.txt` (8131,8132,8133,8134)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8131; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 8133; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 8132; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 8134; Command: awk; Return code: 0; Memory used: 0.0GB
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_keep.txt` (8136)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8136; Command: cut; Return code: 0; Memory used: 0.0GB
> `bedtools sort -i /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks.bed -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_sort.bed` (8138)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8138; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/coverage.flag`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt | uniq > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_coverage.bed` (8141,8142)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.544GB.
PID: 8141; Command: bedtools; Return code: 0; Memory used: 0.011GB
PID: 8142; 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/tutorial1/peak_calling_hg38/tutorial1_peaks_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_coverage.bed > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_norm_peaks_coverage.bed` (8147)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8147; Command: awk; Return code: 0; Memory used: 0.011GB
> `mv /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_norm_peaks_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_coverage.bed` (8151)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8151; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/coverage.flag` (8152)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8152; Command: touch; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_coverage.bed.gz`
> `pigz -f -p 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_coverage.bed > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks_coverage.bed.gz` (8153)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8153; Command: pigz; Return code: 0; Memory used: 0.005GB
### # Produce bigBed formatted narrowPeak file (09-21 14:39:53) elapsed: 7.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/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/tutorial1/peak_calling_hg38/bigNarrowPeak.as` (8176)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8176; Command: echo; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks.bigBed`
> `bedToBigBed -as=/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/bigNarrowPeak.as -type=bed6+4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tmp85spiubq /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/tutorial1_peaks.bigBed` (8177)
pass1 - making usageList (53 chroms): 91 millis
pass2 - checking and writing primary data (352537 records, 10 fields): 875 millis
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8177; Command: bedToBigBed; Return code: 0; Memory used: 0.004GB
### Annotate peaks (09-21 14:39:58) elapsed: 5.0 _TIME_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_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/tutorial1/peak_calling_hg38/tutorial1_peaks_normalized.narrowPeak -f /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_annotations.bed -g hg38 -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_peak_chromosome_distribution.pdf` (8179)
chromosome distribution plot completed!
Command completed. Elapsed time: 0:00:41. Running peak memory: 3.544GB.
PID: 8179; Command: Rscript; Return code: 0; Memory used: 0.459GB
> `Peak chromosome distribution` QC_hg38/tutorial1_peak_chromosome_distribution.pdf Peak chromosome distribution QC_hg38/tutorial1_peak_chromosome_distribution.png PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_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/tutorial1/peak_calling_hg38/tutorial1_peaks_normalized.narrowPeak -f /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_annotations.bed -g hg38 -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_peak_TSS_distribution.pdf` (8659)
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: 0:00:17. Running peak memory: 3.544GB.
PID: 8659; Command: Rscript; Return code: 0; Memory used: 0.497GB
> `TSS distance distribution` QC_hg38/tutorial1_peak_TSS_distribution.pdf TSS distance distribution QC_hg38/tutorial1_peak_TSS_distribution.png PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_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/tutorial1/peak_calling_hg38/tutorial1_peaks_normalized.narrowPeak -f /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_annotations.bed -g hg38 -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_peak_genomic_distribution.pdf` (8724)
genomic distribution plot completed!
Command completed. Elapsed time: 0:00:19. Running peak memory: 3.544GB.
PID: 8724; Command: Rscript; Return code: 0; Memory used: 0.549GB
> `Peak partition distribution` QC_hg38/tutorial1_peak_genomic_distribution.pdf Peak partition distribution QC_hg38/tutorial1_peak_genomic_distribution.png PEPATAC _OBJ_
### Calculate read coverage (09-21 14:41:14) elapsed: 77.0 _TIME_
> `cut -f 4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_annotations.bed | sort -u`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/3' UTR`
> `awk -F' ' '{print>"/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/"$4}' /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/raw/hg38_annotations.bed` (8783)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.544GB.
PID: 8783; Command: awk; Return code: 0; Memory used: 0.005GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/3_UTR`
> `mv "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/3' UTR" "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/3_UTR"` (8787)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8787; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/3_UTR_sort.bed` (8788,8789,8790,8791)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8788; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 8789; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 8791; Command: bedtools; Return code: 0; Memory used: 0.036GB
PID: 8790; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_3_UTR_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/3_UTR_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_3_UTR_coverage.bed` (8803)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.544GB.
PID: 8803; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/5' UTR`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/5_UTR`
> `mv "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/5' UTR" "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/5_UTR"` (8822)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8822; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/5_UTR_sort.bed` (8823,8824,8825,8826)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8823; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 8824; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 8826; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 8825; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_5_UTR_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/5_UTR_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_5_UTR_coverage.bed` (8829)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.544GB.
PID: 8829; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Enhancer`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Enhancer_sort.bed` (8839,8840,8841,8842)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8839; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 8841; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 8840; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 8842; Command: bedtools; Return code: 0; Memory used: 0.047GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Enhancer_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Enhancer_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Enhancer_coverage.bed` (8860)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.544GB.
PID: 8860; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Exon`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Exon_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Exon_sort.bed` (8864,8865,8866,8867)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.544GB.
PID: 8864; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 8865; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 8867; Command: bedtools; Return code: 0; Memory used: 0.167GB
PID: 8866; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Exon_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Exon_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Exon_coverage.bed` (8878)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.544GB.
PID: 8878; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Intron`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Intron_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Intron_sort.bed` (8886,8887,8888,8889)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.544GB.
PID: 8886; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 8889; Command: bedtools; Return code: 0; Memory used: 0.076GB
PID: 8887; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 8888; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Intron_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Intron_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Intron_coverage.bed` (8894)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.544GB.
PID: 8894; Command: bedtools; Return code: 0; Memory used: 0.014GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter_sort.bed` (8901,8902,8903,8904)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8901; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 8902; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 8904; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 8903; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Promoter_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Promoter_coverage.bed` (8906)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.544GB.
PID: 8906; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target exists: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter Flanking Region`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter_Flanking_Region`
> `mv "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter Flanking Region" "/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter_Flanking_Region"` (8912)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.544GB.
PID: 8912; Command: mv; Return code: 0; Memory used: 0.001GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt | grep -wf - /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter_Flanking_Region_sort.bed` (8913,8914,8915,8916)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.544GB.
PID: 8913; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 8915; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 8914; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 8916; Command: bedtools; Return code: 0; Memory used: 0.05GB
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Promoter_Flanking_Region_coverage.bed`
> `bedtools coverage -sorted -a /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/Promoter_Flanking_Region_sort.bed -b /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam -g /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/peak_calling_hg38/chr_order.txt > /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Promoter_Flanking_Region_coverage.bed` (8921)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.544GB.
PID: 8921; Command: bedtools; Return code: 0; Memory used: 0.008GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (09-21 14:41:46) elapsed: 32.0 _TIME_
> `samtools view -@ 4 -q 10 -c -F4 /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/aligned_hg38/tutorial1_sort_dedup.bam`
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_cFRiF.pdf`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R frif -s tutorial1 -z 3099922541 -n 876930 -y cfrif --reads -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_cFRiF.pdf --bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_3_UTR_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_5_UTR_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Enhancer_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Exon_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Intron_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Promoter_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Promoter_Flanking_Region_coverage.bed` (8933)
FRiF plot completed!
Command completed. Elapsed time: 0:00:40. Running peak memory: 3.544GB.
PID: 8933; Command: Rscript; Return code: 0; Memory used: 0.536GB
> `cFRiF` QC_hg38/tutorial1_cFRiF.pdf cFRiF QC_hg38/tutorial1_cFRiF.png PEPATAC _OBJ_
Target to produce: `/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_FRiF.pdf`
> `Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC.R frif -s tutorial1 -z 3099922541 -n 876930 -y frif --reads -o /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_FRiF.pdf --bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_3_UTR_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_5_UTR_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Enhancer_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Exon_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Intron_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Promoter_coverage.bed /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline/tutorial1/QC_hg38/tutorial1_Promoter_Flanking_Region_coverage.bed` (9012)
FRiF plot completed!
Command completed. Elapsed time: 0:00:35. Running peak memory: 3.544GB.
PID: 9012; Command: Rscript; Return code: 0; Memory used: 0.54GB
> `FRiF` QC_hg38/tutorial1_FRiF.pdf FRiF QC_hg38/tutorial1_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): 0:38:48
* Total elapsed time (all runs): 0:53:54
* Peak memory (this run): 3.5437 GB
* Pipeline completed time: 2020-09-21 14:43:02