### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_GRO-seq --genome hg38 --input /project/shefflab/data//sra_fastq/SRR1552484.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol GRO --umi-len 0 --scale --prealignments human_rDNA --dirty`
* Compute host: udc-aj38-17c0
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/
* Pipeline started at: (06-11 17:29:51) elapsed: 0.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//sra_fastq/SRR1552484.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `12000`
* `new_start`: `False`
* `no_fifo`: `False`
* `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline`
* `paired_end`: `False`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `GRO`
* `recover`: `False`
* `sample_name`: `K562_GRO-seq`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `SINGLE`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `0`
* `verbosity`: `None`
----------------------------------------
Local input file: /project/shefflab/data//sra_fastq/SRR1552484.fastq.gz
> `File_mb` 1322.25 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected GRO input
### Merge/link and fastq conversion: (06-11 17:29:53) elapsed: 2.0 _TIME_
Number of input file sets: 1
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz`
> `ln -sf /project/shefflab/data//sra_fastq/SRR1552484.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz` (347126)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 347126; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz'
Found .fastq.gz file
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1.fastq`
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1.fastq` (347127)
Command completed. Elapsed time: 0:01:06. Running peak memory: 0.002GB.
PID: 347127; Command: pigz; Return code: 0; Memory used: 0.002GB
> `Raw_reads` 30363736 PEPPRO _RES_
> `Fastq_reads` 30363736 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz']
### FASTQ processing: (06-11 17:31:22) elapsed: 89.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1_processed.fastq`
> `(cutadapt -j 12 -m 2 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt` (347505)
Command completed. Elapsed time: 0:00:42. Running peak memory: 2.13GB.
PID: 347505; Command: cutadapt; Return code: 0; Memory used: 2.13GB
> `seqtk trimfq -b 0 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1_noadap.fastq | seqtk seq -L 2 - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1_processed.fastq` (347576,347578)
Command completed. Elapsed time: 0:01:00. Running peak memory: 2.13GB.
PID: 347576; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 347578; Command: seqtk; Return code: 0; Memory used: 0.002GB
> `grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 22296806.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `awk '{sum+=$1*$2} END {printf "%.0f", sum}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 1041369.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 3.4296 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastqc/K562_GRO-seq_R1_processed_fastqc.html`
> `echo '### Calculate the number of trimmed reads'` (347706)
### Calculate the number of trimmed reads
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.13GB.
PID: 347706; Command: echo; Return code: 0; Memory used: 0.0GB
Evaluating read trimming
> `Trimmed_reads` 29322367 PEPPRO _RES_
> `Trim_loss_rate` 3.43 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1_processed.fastq` (347737)
Started analysis of K562_GRO-seq_R1_processed.fastq
Approx 5% complete for K562_GRO-seq_R1_processed.fastq
Approx 10% complete for K562_GRO-seq_R1_processed.fastq
Approx 15% complete for K562_GRO-seq_R1_processed.fastq
Approx 20% complete for K562_GRO-seq_R1_processed.fastq
Approx 25% complete for K562_GRO-seq_R1_processed.fastq
Approx 30% complete for K562_GRO-seq_R1_processed.fastq
Approx 35% complete for K562_GRO-seq_R1_processed.fastq
Approx 40% complete for K562_GRO-seq_R1_processed.fastq
Approx 45% complete for K562_GRO-seq_R1_processed.fastq
Approx 50% complete for K562_GRO-seq_R1_processed.fastq
Approx 55% complete for K562_GRO-seq_R1_processed.fastq
Approx 60% complete for K562_GRO-seq_R1_processed.fastq
Approx 65% complete for K562_GRO-seq_R1_processed.fastq
Approx 70% complete for K562_GRO-seq_R1_processed.fastq
Approx 75% complete for K562_GRO-seq_R1_processed.fastq
Approx 80% complete for K562_GRO-seq_R1_processed.fastq
Approx 85% complete for K562_GRO-seq_R1_processed.fastq
Approx 90% complete for K562_GRO-seq_R1_processed.fastq
Approx 95% complete for K562_GRO-seq_R1_processed.fastq
Analysis complete for K562_GRO-seq_R1_processed.fastq
Command completed. Elapsed time: 0:01:29. Running peak memory: 2.13GB.
PID: 347737; Command: fastqc; Return code: 0; Memory used: 0.165GB
> `FastQC report r1` fastqc/K562_GRO-seq_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/processed_R1.flag` (348047)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.13GB.
PID: 348047; Command: touch; Return code: 0; Memory used: 0.0GB
### Plot adapter insertion distribution (06-11 17:35:38) elapsed: 256.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_adapter_insertion_distribution.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R cutadapt -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt` (348048)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:11. Running peak memory: 2.13GB.
PID: 348048; Command: Rscript; Return code: 0; Memory used: 0.112GB
> `Adapter insertion distribution` cutadapt/K562_GRO-seq_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_GRO-seq_R1_adapter_insertion_distribution.png PEPPRO _OBJ_
Missing stat 'Peak_adapter_insertion_size'
> `awk '/count/,0' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt | awk 'NR>2 {print prev} {prev=$0}' | awk '{if ($3/$2 < 0.01) print $1, $2}' | awk 'BEGIN{max= 0; max_len=0; len=0}{if ($2>0+max) {max=$2; len=$1}; max_len=$1} END{print max_len-len}'`
> `Peak_adapter_insertion_size` 22 PEPPRO _RES_
Missing stat 'Degradation_ratio'
### Calculating degradation ratio (06-11 17:35:49) elapsed: 11.0 _TIME_
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt | awk '{ if ($1 == 10) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt | awk '{ if ($1 == 20) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt | awk '{ if ($1 == 30) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt | awk '{ if ($1 == 40) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk '/count/,0' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_cutadapt.txt | awk 'NR>2 {print prev} {prev=$0}' | awk '{if ($3/$2 < 0.01) print $1, $2}' | awk '{a[NR]=$1; b[NR]=$2; max_len=$1}{if ($1 > max_len) {max_len=$1}} END{ for (i in a) print 1+max_len-a[i], b[i]}' | sort -nk1 | awk '($1 <= 20 && $1 >= 10){degradedSum += $2}; ($1 >= 30 && $1 <= 40){intactSum += $2} END {if (intactSum < 1) {intactSum = 1} print degradedSum/intactSum}'`
> `Degradation_ratio` 0.7189 PEPPRO _RES_
### Prealignments (06-11 17:35:49) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-11 17:35:49) elapsed: 0.0 _TIME_
> `(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id K562_GRO-seq -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/prealignments/K562_GRO-seq_human_rDNA_unmap.fq 2>&1 > /dev/null)`
Missing stat 'Aligned_reads_human_rDNA'
29322367 reads; of these:
29322367 (100.00%) were unpaired; of these:
25012896 (85.30%) aligned 0 times
4309471 (14.70%) aligned exactly 1 time
0 (0.00%) aligned >1 times
14.70% overall alignment rate
> `Aligned_reads_human_rDNA` 4309471.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 14.7 PEPPRO _RES_
### Map to genome (06-11 17:39:22) elapsed: 213.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam`
> `bowtie2 -p 12 --very-sensitive --rg-id K562_GRO-seq -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/prealignments/K562_GRO-seq_human_rDNA_unmap.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/tmpuee4zdhj -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_temp.bam` (348363,348364,348365)
25012896 reads; of these:
25012896 (100.00%) were unpaired; of these:
2113226 (8.45%) aligned 0 times
15215880 (60.83%) aligned exactly 1 time
7683790 (30.72%) aligned >1 times
91.55% overall alignment rate
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:10:14. Running peak memory: 3.668GB.
PID: 348363; Command: bowtie2; Return code: 0; Memory used: 3.668GB
PID: 348364; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 348365; Command: samtools; Return code: 0; Memory used: 0.902GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam` (349569)
Command completed. Elapsed time: 0:00:54. Running peak memory: 3.668GB.
PID: 349569; Command: samtools; Return code: 0; Memory used: 0.018GB
> `samtools depth -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 22899670 PEPPRO _RES_
> `QC_filtered_reads` 4468262 PEPPRO _RES_
> `Aligned_reads` 18431408 PEPPRO _RES_
> `Alignment_rate` 62.86 PEPPRO _RES_
> `Total_efficiency` 60.7 PEPPRO _RES_
> `Read_depth` 2.65 PEPPRO _RES_
### Compress all unmapped read files (06-11 18:00:14) elapsed: 1252.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/prealignments/K562_GRO-seq_human_rDNA_unmap.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/prealignments/K562_GRO-seq_human_rDNA_unmap.fq` (351183)
Command completed. Elapsed time: 0:00:47. Running peak memory: 3.668GB.
PID: 351183; Command: pigz; Return code: 0; Memory used: 0.013GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_temp.bam` (351262)
Command completed. Elapsed time: 0:00:18. Running peak memory: 3.668GB.
PID: 351262; Command: samtools; Return code: 0; Memory used: 0.017GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 843399 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam` (351285)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.668GB.
PID: 351285; Command: samtools; Return code: 0; Memory used: 0.016GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam | cut -f 1-2 | awk '{print $1, 0, $2}' | grep -vwe 'chrM' -vwe 'chrMT' -vwe 'M' -vwe 'MT' -vwe 'rCRSd' -vwe 'rCRSd_3k' > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/chr_sizes.bed` (351301,351302,351303,351304)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.668GB.
PID: 351301; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 351303; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 351302; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 351304; Command: grep; Return code: 0; Memory used: 0.0GB
> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_noMT.bam` (351307)
Command completed. Elapsed time: 0:00:32. Running peak memory: 3.668GB.
PID: 351307; Command: samtools; Return code: 0; Memory used: 0.019GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam` (351355)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.668GB.
PID: 351355; Command: mv; Return code: 0; Memory used: 0.001GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam` (351356)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.668GB.
PID: 351356; Command: samtools; Return code: 0; Memory used: 0.014GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-`
> `Maximum_read_length` 50 PEPPRO _RES_
Missing stat 'Genome_size'
> `awk '{sum+=$2} END {printf "%.0f", sum}' /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes`
> `Genome_size` 3099922541 PEPPRO _RES_
### Calculate NRF, PBC1, and PBC2 (06-11 18:03:14) elapsed: 180.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam.bai`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_bamQC.tsv`
> `/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_bamQC.tsv` (351434)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/tmp_K562_GRO-seq_sort_gbhq8men'
Processing with 12 cores...
Discarding 91 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr22_KI270737v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270581v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1']
Keeping 104 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270511v1', 'chrUn_KI270583v1', 'chrUn_KI270580v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270374v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Command completed. Elapsed time: 0:00:34. Running peak memory: 3.668GB.
PID: 351434; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.057GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_bamQC.tsv`
> `NRF` 0.7 PEPPRO _RES_
> `PBC1` 0.86 PEPPRO _RES_
> `PBC2` 8.69 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_unmap.bam`
> `samtools view -b -@ 12 -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_unmap.bam` (351500)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.668GB.
PID: 351500; Command: samtools; Return code: 0; Memory used: 0.016GB
> `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_temp.bam`
> `Unmapped_reads` 2113226 PEPPRO _RES_
### Split BAM by strand (06-11 18:03:58) elapsed: 44.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam` (351538)
Command completed. Elapsed time: 0:01:06. Running peak memory: 3.668GB.
PID: 351538; Command: samtools; Return code: 0; Memory used: 0.006GB
> `samtools view -bh -f 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam` (351800)
Command completed. Elapsed time: 0:01:03. Running peak memory: 3.668GB.
PID: 351800; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-11 18:06:07) elapsed: 129.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (351866)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.668GB.
PID: 351866; Command: sed; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_plus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_plus_TssEnrichment.txt` (351867)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.668GB.
PID: 351867; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.599GB
> `TSS_coding_score` 23.9 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_minus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_minus_TssEnrichment.txt` (351903)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.668GB.
PID: 351903; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.746GB
> `TSS_non-coding_score` 8.6 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSSenrichment.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_minus_TssEnrichment.txt` (351934)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_minus_TssEnrichment.txt
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
TSS enrichment plot completed!
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.668GB.
PID: 351934; Command: Rscript; Return code: 0; Memory used: 0.102GB
> `TSS enrichment` QC_hg38/K562_GRO-seq_TSSenrichment.pdf TSS enrichment QC_hg38/K562_GRO-seq_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam | grep 'SN:' | awk -F':' '{print $2,$3}' | awk -F' ' -v OFS=' ' '{print $1,$3}' > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt` (351961,351962,351963,351964)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.668GB.
PID: 351961; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 351963; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 351962; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 351964; Command: awk; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_keep.txt` (351967)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.668GB.
PID: 351967; Command: cut; Return code: 0; Memory used: 0.002GB
### Calculate Pause Index (PI) (06-11 18:06:32) elapsed: 25.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_TSS.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_tss.bed` (351969,351970)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.668GB.
PID: 351969; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 351970; Command: bedtools; Return code: 0; Memory used: 0.094GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_gene_body.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed` (351974,351975)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.668GB.
PID: 351974; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 351975; Command: bedtools; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4,4 -k7,7nr | sort -k4,4 -u > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSS_density.bed` (351979,351980,351981,351982)
Command completed. Elapsed time: 0:00:26. Running peak memory: 3.668GB.
PID: 351979; Command: bedtools; Return code: 0; Memory used: 0.014GB
PID: 351981; Command: sort; Return code: 0; Memory used: 0.005GB
PID: 351980; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 351982; Command: sort; Return code: 0; Memory used: 0.003GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_gene_body_density.bed` (352009,352010,352012)
Command completed. Elapsed time: 0:00:38. Running peak memory: 3.668GB.
PID: 352012; Command: sort; Return code: 0; Memory used: 0.007GB
PID: 352009; Command: bedtools; Return code: 0; Memory used: 0.051GB
PID: 352010; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.bed`
awk: cmd. line:1: { if ($5 == ){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}
awk: cmd. line:1: ^ syntax error
awk: cmd. line:1: { if ($5 == ){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}
awk: cmd. line:1: ^ syntax error
> `join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_gene_body_density.bed | awk -v OFS=' ' '{ if ($5 == ){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}' | env LC_COLLATE=C sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/tmpxwvopkcb` (352054,352055,352056)
Got SIGTERM. Failing gracefully... (06-11 18:55:15) elapsed: 2923.0 _TIME_
Child process 352054 (join) terminated after 0 sec.
Setting dynamic recover file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/recover.lock.QC_hg38__K562_GRO-seq_pause_index.bed
### Pipeline failed at: (06-11 18:55:15) elapsed: 0.0 _TIME_
Total time: 1:25:24
Failure reason: SIGTERM
Pipeline aborted.
### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_GRO-seq --genome hg38 --input /project/shefflab/data//sra_fastq/SRR1552484.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol GRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba26-16
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/
* Pipeline started at: (06-11 19:10:15) elapsed: 0.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//sra_fastq/SRR1552484.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `12000`
* `new_start`: `False`
* `no_fifo`: `False`
* `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline`
* `paired_end`: `False`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `GRO`
* `recover`: `True`
* `sample_name`: `K562_GRO-seq`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `SINGLE`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `0`
* `verbosity`: `None`
----------------------------------------
Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//sra_fastq/SRR1552484.fastq.gz
> `File_mb` 1322.25 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected GRO input
### Merge/link and fastq conversion: (06-11 19:10:15) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz'
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz']
### FASTQ processing: (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/processed_R1.flag`
### Plot adapter insertion distribution (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_adapter_insertion_distribution.pdf`
> `Adapter insertion distribution` cutadapt/K562_GRO-seq_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_GRO-seq_R1_adapter_insertion_distribution.png PEPPRO _OBJ_
### Prealignments (06-11 19:10:15) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-11 19:10:15) elapsed: 0.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/prealignments/K562_GRO-seq_human_rDNA_unmap.fq
### Map to genome (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam`
### Compress all unmapped read files (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/prealignments/K562_GRO-seq_human_rDNA_unmap.fq.gz`
### Calculate NRF, PBC1, and PBC2 (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam.bai`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_bamQC.tsv`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_unmap.bam`
### Split BAM by strand (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam`
### Calculate TSS enrichment (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSSenrichment.pdf`
> `TSS enrichment` QC_hg38/K562_GRO-seq_TSSenrichment.pdf TSS enrichment QC_hg38/K562_GRO-seq_TSSenrichment.png PEPPRO _OBJ_
### Calculate Pause Index (PI) (06-11 19:10:15) elapsed: 0.0 _TIME_
Missing stat 'Pause_index'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_tss.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSS_density.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_gene_body_density.bed`
Found lock file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/lock.QC_hg38__K562_GRO-seq_pause_index.bed
Overwriting target...
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.bed`
> `join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_gene_body_density.bed | awk -v OFS=' ' '{ if ($5 == "+"){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2), ($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}' | env LC_COLLATE=C sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/tmpnu6wpr_c` (71328,71329,71330)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.006GB.
PID: 71328; Command: join; Return code: 0; Memory used: 0.001GB
PID: 71330; Command: env; Return code: 0; Memory used: 0.006GB
PID: 71329; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/tmpnu6wpr_c | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}`
/bin/sh: -c: line 0: unexpected EOF while looking for matching `''
/bin/sh: -c: line 1: syntax error: unexpected end of file
### Pipeline failed at: (06-11 19:10:16) elapsed: 0.0 _TIME_
Total time: 0:00:01
Failure reason: Command 'awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/tmpnu6wpr_c | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}' returned non-zero exit status 1.
### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_GRO-seq --genome hg38 --input /project/shefflab/data//sra_fastq/SRR1552484.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol GRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-aj37-18c0
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/
* Pipeline started at: (06-14 21:14:10) elapsed: 9.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//sra_fastq/SRR1552484.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `12000`
* `new_start`: `False`
* `no_fifo`: `False`
* `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline`
* `paired_end`: `False`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `GRO`
* `recover`: `True`
* `sample_name`: `K562_GRO-seq`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `SINGLE`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `0`
* `verbosity`: `None`
----------------------------------------
Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//sra_fastq/SRR1552484.fastq.gz
> `File_mb` 1322.25 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected GRO input
### Merge/link and fastq conversion: (06-14 21:14:11) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz'
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/K562_GRO-seq_R1.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/K562_GRO-seq.fastq.gz']
### FASTQ processing: (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/fastq/processed_R1.flag`
### Plot adapter insertion distribution (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/cutadapt/K562_GRO-seq_R1_adapter_insertion_distribution.pdf`
> `Adapter insertion distribution` cutadapt/K562_GRO-seq_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_GRO-seq_R1_adapter_insertion_distribution.png PEPPRO _OBJ_
### Prealignments (06-14 21:14:11) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-14 21:14:11) elapsed: 0.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/prealignments/K562_GRO-seq_human_rDNA_unmap.fq
### Map to genome (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam`
### Compress all unmapped read files (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/prealignments/K562_GRO-seq_human_rDNA_unmap.fq.gz`
### Calculate NRF, PBC1, and PBC2 (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam.bai`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_bamQC.tsv`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_unmap.bam`
### Split BAM by strand (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam`
### Calculate TSS enrichment (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSSenrichment.pdf`
> `TSS enrichment` QC_hg38/K562_GRO-seq_TSSenrichment.pdf TSS enrichment QC_hg38/K562_GRO-seq_TSSenrichment.png PEPPRO _OBJ_
### Calculate Pause Index (PI) (06-14 21:14:11) elapsed: 0.0 _TIME_
Missing stat 'Pause_index'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_tss.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSS_density.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_gene_body_density.bed`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.bed`
> `join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_gene_body_density.bed | awk -v OFS=' ' '{ if ($5 == "+"){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2), ($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}' | env LC_COLLATE=C sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/tmp4yy_drxc` (428183,428191,428201)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.004GB.
PID: 428183; Command: join; Return code: 0; Memory used: 0.001GB
PID: 428201; Command: env; Return code: 0; Memory used: 0.004GB
PID: 428191; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/tmp4yy_drxc | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}'`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.0172824) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/tmp4yy_drxc > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.bed` (428280)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.004GB.
PID: 428280; Command: awk; Return code: 0; Memory used: 0.002GB
> `sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.bed | awk ' { a[i++]=$5; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'`
> `Pause_index` 10.74 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R pi --annotate -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.bed` (428320)
Pause index plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.287GB.
PID: 428320; Command: Rscript; Return code: 0; Memory used: 0.287GB
> `Pause index` QC_hg38/K562_GRO-seq_pause_index.pdf Pause index QC_hg38/K562_GRO-seq_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_pause_index.bed` (429780)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.287GB.
PID: 429780; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-14 21:14:18) elapsed: 6.0 _TIME_
Missing stat 'Plus_FRiP'
> `samtools view -@ 4 -c -L /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam`
18431408 6290701
> `Plus_FRiP` 0.34 PEPPRO _RES_
Missing stat 'Minus_FRiP'
> `samtools view -@ 4 -c -L /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam`
18431408 5983864
> `Minus_FRiP` 0.32 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_gene_sort.bed` (430842,430843)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.287GB.
PID: 430842; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 430843; Command: bedtools; Return code: 0; Memory used: 0.005GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_gene_coverage.bed` (430845)
Command completed. Elapsed time: 0:00:27. Running peak memory: 0.287GB.
PID: 430845; Command: bedtools; Return code: 0; Memory used: 0.074GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/hg38_annotations.bed`
> `ln -sf /project/shefflab/genomes/hg38/feat_annotation/default/hg38_annotations.bed.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/hg38_annotations.bed.gz` (431095)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.287GB.
PID: 431095; Command: ln; Return code: 0; Memory used: 0.0GB
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/hg38_annotations.bed` (431096)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.287GB.
PID: 431096; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-14 21:15:17) elapsed: 60.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/raw/hg38_annotations.bed` (431105)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.287GB.
PID: 431105; Command: awk; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Enhancer_sort.bed` (431108,431109,431111,431113)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.287GB.
PID: 431108; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431109; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 431113; Command: bedtools; Return code: 0; Memory used: 0.012GB
PID: 431111; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Enhancer_plus_coverage.bed` (431115)
Command completed. Elapsed time: 0:00:11. Running peak memory: 0.287GB.
PID: 431115; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Enhancer_minus_coverage.bed` (431133)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.287GB.
PID: 431133; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_sort.bed` (431145,431146,431147,431148)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.287GB.
PID: 431145; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431146; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 431148; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 431147; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_plus_coverage.bed` (431150)
Command completed. Elapsed time: 0:00:11. Running peak memory: 0.287GB.
PID: 431150; Command: bedtools; Return code: 0; Memory used: 0.025GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_minus_coverage.bed` (431171)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.287GB.
PID: 431171; Command: bedtools; Return code: 0; Memory used: 0.027GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_Flanking_Region"` (431197)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.287GB.
PID: 431197; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed` (431198,431199,431200,431201)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.287GB.
PID: 431198; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431200; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 431199; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 431201; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_Flanking_Region_plus_coverage.bed` (431204)
Command completed. Elapsed time: 0:00:11. Running peak memory: 0.287GB.
PID: 431204; Command: bedtools; Return code: 0; Memory used: 0.013GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_Flanking_Region_minus_coverage.bed` (431228)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.287GB.
PID: 431228; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/5_UTR"` (431248)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.287GB.
PID: 431248; Command: mv; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/5_UTR_sort.bed` (431249,431250,431251,431252)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.287GB.
PID: 431249; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431250; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 431252; Command: bedtools; Return code: 0; Memory used: 0.01GB
PID: 431251; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_5_UTR_plus_coverage.bed` (431255)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.287GB.
PID: 431255; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_5_UTR_minus_coverage.bed` (431268)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.287GB.
PID: 431268; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/3_UTR"` (431285)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.287GB.
PID: 431285; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/3_UTR_sort.bed` (431286,431287,431288,431289)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.287GB.
PID: 431286; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431287; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 431289; Command: bedtools; Return code: 0; Memory used: 0.035GB
PID: 431288; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_3_UTR_plus_coverage.bed` (431291)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.287GB.
PID: 431291; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_3_UTR_minus_coverage.bed` (431349)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.287GB.
PID: 431349; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Exon_sort.bed` (436564,436572,436585,436590)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.287GB.
PID: 436564; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 436572; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 436590; Command: bedtools; Return code: 0; Memory used: 0.172GB
PID: 436585; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Exon_plus_coverage.bed` (439659)
Command completed. Elapsed time: 0:00:13. Running peak memory: 0.287GB.
PID: 439659; Command: bedtools; Return code: 0; Memory used: 0.018GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Exon_minus_coverage.bed` (456903)
Command completed. Elapsed time: 0:00:12. Running peak memory: 0.287GB.
PID: 456903; Command: bedtools; Return code: 0; Memory used: 0.021GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Intron_sort.bed` (14009,14016,14019,14023)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.287GB.
PID: 14009; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 14019; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 14016; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 14023; Command: bedtools; Return code: 0; Memory used: 0.078GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Intron_plus_coverage.bed` (15300)
Command completed. Elapsed time: 0:00:13. Running peak memory: 0.287GB.
PID: 15300; Command: bedtools; Return code: 0; Memory used: 0.02GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Intron_minus_coverage.bed` (17150)
Command completed. Elapsed time: 0:00:13. Running peak memory: 0.287GB.
PID: 17150; Command: bedtools; Return code: 0; Memory used: 0.028GB
### Plot cFRiF/FRiF (06-14 21:18:00) elapsed: 163.0 _TIME_
> `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_GRO-seq -z 3099922541 -n 9058650 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Intron_plus_coverage.bed` (21478)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:35. Running peak memory: 0.462GB.
PID: 21478; Command: Rscript; Return code: 0; Memory used: 0.462GB
> `cFRiF` QC_hg38/K562_GRO-seq_cFRiF.pdf cFRiF QC_hg38/K562_GRO-seq_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_GRO-seq -z 3099922541 -n 9058650 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_Intron_plus_coverage.bed` (53701)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:25. Running peak memory: 0.507GB.
PID: 53701; Command: Rscript; Return code: 0; Memory used: 0.507GB
> `FRiF` QC_hg38/K562_GRO-seq_FRiF.pdf FRiF QC_hg38/K562_GRO-seq_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-14 21:19:00) elapsed: 61.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_exons.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_exons_sort.bed` (61345,61346)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.507GB.
PID: 61345; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 61346; Command: bedtools; Return code: 0; Memory used: 0.099GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_introns.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_introns_sort.bed` (61352,61353,61354)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.507GB.
PID: 61352; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 61354; Command: bedtools; Return code: 0; Memory used: 0.006GB
PID: 61353; Command: bedtools; Return code: 0; Memory used: 0.036GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exons_coverage.bed` (61366)
Command completed. Elapsed time: 0:00:20. Running peak memory: 0.507GB.
PID: 61366; Command: bedtools; Return code: 0; Memory used: 0.047GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_introns_coverage.bed` (61487)
Command completed. Elapsed time: 0:00:23. Running peak memory: 0.507GB.
PID: 61487; Command: bedtools; Return code: 0; Memory used: 0.033GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exons_rpkm.bed`
> `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/18.431408)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exons_rpkm.bed` (61511,61512,61513)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.507GB.
PID: 61511; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 61513; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 61512; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_introns_rpkm.bed`
> `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/18.431408)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_introns_rpkm.bed` (61516,61517,61518)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.507GB.
PID: 61516; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 61518; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 61517; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exons_rpkm.bed | awk -v OFS=' ' 'NF==11 {print $7, $8, $9, $1, ($10/$5), $11}' | sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exon_intron_ratios.bed` (61521,61522,61523)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.507GB.
PID: 61521; Command: join; Return code: 0; Memory used: 0.001GB
PID: 61523; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 61522; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exon_intron_ratios.bed | sort -n | awk ' { a[i++]=$1; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'`
> `mRNA_contamination` 1.33 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_mRNA_contamination.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exon_intron_ratios.bed --annotate` (61529)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:04. Running peak memory: 0.507GB.
PID: 61529; Command: Rscript; Return code: 0; Memory used: 0.323GB
> `mRNA contamination` QC_hg38/K562_GRO-seq_mRNA_contamination.pdf mRNA contamination QC_hg38/K562_GRO-seq_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exon_intron_ratios.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/QC_hg38/K562_GRO-seq_exon_intron_ratios.bed` (61559)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.507GB.
PID: 61559; Command: pigz; Return code: 0; Memory used: 0.005GB
### Produce bigWig files (06-14 21:19:59) elapsed: 58.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam` (61567)
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.507GB.
PID: 61567; Command: samtools; Return code: 0; Memory used: 0.01GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_plus_smooth_body_0-mer.bw -p 8 --variable-step --scale 18431408.0` (61790)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_plus.bam'
Temporary files will be stored in: 'tmp_K562_GRO-seq_plus_cuttrace_pp7ztq7s'
Processing with 4 cores...
stdin is empty of data
stdin is empty of data
Discarding 100 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr14_KI270723v1_random', 'chr22_KI270735v1_random', 'chr22_KI270737v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270581v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1']
Keeping 95 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270511v1', 'chrUn_KI270580v1', 'chrUn_KI270579v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270374v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 95 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_plus_exact_body_0-mer.bw'
Merging 95 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:07:24. Running peak memory: 2.62GB.
PID: 61790; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.62GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam` (239914)
Command completed. Elapsed time: 0:00:06. Running peak memory: 2.62GB.
PID: 239914; Command: samtools; Return code: 0; Memory used: 0.01GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_minus_smooth_body_0-mer.bw -p 8 --variable-step --scale 18431408.0` (239935)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/aligned_hg38/K562_GRO-seq_minus.bam'
Temporary files will be stored in: 'tmp_K562_GRO-seq_minus_cuttrace_1axk6ebz'
Processing with 4 cores...
stdin is empty of data
Discarding 111 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr11_KI270721v1_random', 'chr17_KI270730v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270593v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1']
Keeping 84 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270583v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 84 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_minus_exact_body_0-mer.bw'
Merging 84 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_GRO-seq/signal_hg38/K562_GRO-seq_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:07:16. Running peak memory: 2.732GB.
PID: 239935; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.732GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:20:51
* Total elapsed time (all runs): 0:58:31
* Peak memory (this run): 2.7315 GB
* Pipeline completed time: 2020-06-14 21:34:52