### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_PRO-seq_90 --genome hg38 --input /project/shefflab/data//guertin/fastq/K562_PRO_90pct.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 32 -M 32000 --protocol PRO --umi-len 0 --scale --prealignments human_rDNA --dirty`
* Compute host: udc-aj40-16c1
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/
* Pipeline started at: (06-11 17:07:56) elapsed: 4.0 _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`: `32`
* `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//guertin/fastq/K562_PRO_90pct.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `32000`
* `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`: `PRO`
* `recover`: `False`
* `sample_name`: `K562_PRO-seq_90`
* `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//guertin/fastq/K562_PRO_90pct.fastq.gz
> `File_mb` 32665.2 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-11 17:07:57) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/K562_PRO_90pct.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz` (73933)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 73933; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz'
Found .fastq.gz file
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1.fastq`
> `pigz -f -p 32 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1.fastq` (73934)
Command completed. Elapsed time: 0:14:40. Running peak memory: 0.003GB.
PID: 73934; Command: pigz; Return code: 0; Memory used: 0.003GB
> `Raw_reads` 446930263 PEPPRO _RES_
> `Fastq_reads` 446930263 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz']
### FASTQ processing: (06-11 17:53:02) elapsed: 2705.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_processed.fastq`
> `(cutadapt -j 32 -m 2 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/cutadapt/K562_PRO-seq_90_R1_cutadapt.txt` (78713)
Command completed. Elapsed time: 0:26:15. Running peak memory: 13.41GB.
PID: 78713; Command: cutadapt; Return code: 0; Memory used: 13.41GB
> `seqtk trimfq -b 0 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_noadap.fastq | seqtk seq -L 2 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_processed.fastq` (81973,81974)
Command completed. Elapsed time: 0:14:32. Running peak memory: 13.41GB.
PID: 81973; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 81974; Command: seqtk; Return code: 0; Memory used: 0.002GB
> `grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/cutadapt/K562_PRO-seq_90_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 380755198.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/cutadapt/K562_PRO-seq_90_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_PRO-seq_90/cutadapt/K562_PRO-seq_90_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 11194446.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 2.5047 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastqc/K562_PRO-seq_90_R1_processed_fastqc.html`
> `echo '### Calculate the number of trimmed reads'` (85528)
### Calculate the number of trimmed reads
Command completed. Elapsed time: 0:00:00. Running peak memory: 13.41GB.
PID: 85528; Command: echo; Return code: 0; Memory used: 0.0GB
Evaluating read trimming
> `Trimmed_reads` 435735817 PEPPRO _RES_
> `Trim_loss_rate` 2.5 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_processed.fastq` (85722)
Started analysis of K562_PRO-seq_90_R1_processed.fastq
Approx 5% complete for K562_PRO-seq_90_R1_processed.fastq
Got SIGTERM. Failing gracefully... (06-11 18:55:14) elapsed: 3732.0 _TIME_
Child process 85722 (fastqc) terminated after 0 sec.
Setting dynamic recover file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/recover.lock.fastqc__K562_PRO-seq_90_R1_processed_fastqc.html
Setting dynamic recover file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/recover.lock.trimmed_fastqc
### Pipeline failed at: (06-11 18:55:14) elapsed: 0.0 _TIME_
Total time: 1:47:22
Failure reason: SIGTERM
Pipeline aborted.
### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_PRO-seq_90 --genome hg38 --input /project/shefflab/data//guertin/fastq/K562_PRO_90pct.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 32 -M 32000 --protocol PRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-aj40-14c1
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/
* Pipeline started at: (06-11 19:07:43) elapsed: 3.0 _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`: `32`
* `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//guertin/fastq/K562_PRO_90pct.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `32000`
* `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`: `PRO`
* `recover`: `True`
* `sample_name`: `K562_PRO-seq_90`
* `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_PRO-seq_90/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//guertin/fastq/K562_PRO_90pct.fastq.gz
> `File_mb` 32665.2 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-11 19:07:44) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz'
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz']
### FASTQ processing: (06-11 19:07:44) elapsed: 0.0 _TIME_
> `cutadapt --version`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_processed.fastq`
Found lock file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/lock.fastqc__K562_PRO-seq_90_R1_processed_fastqc.html
Overwriting target...
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastqc/K562_PRO-seq_90_R1_processed_fastqc.html`
> `echo '### Calculate the number of trimmed reads'` (139941)
### Calculate the number of trimmed reads
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 139941; Command: echo; Return code: 0; Memory used: 0.0GB
Evaluating read trimming
> `Trimmed_reads` 435735817 PEPPRO _RES_
> `Trim_loss_rate` 2.5 PEPPRO _RES_
Found lock file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/lock.trimmed_fastqc
Overwriting target...
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_processed.fastq` (140400)
Started analysis of K562_PRO-seq_90_R1_processed.fastq
Approx 5% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 10% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 15% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 20% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 25% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 30% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 35% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 40% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 45% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 50% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 55% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 60% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 65% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 70% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 75% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 80% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 85% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 90% complete for K562_PRO-seq_90_R1_processed.fastq
Approx 95% complete for K562_PRO-seq_90_R1_processed.fastq
Analysis complete for K562_PRO-seq_90_R1_processed.fastq
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007fcf72597bd4, pid=140400, tid=0x00007fcf4f2f2700
#
# JRE version: Java(TM) SE Runtime Environment (8.0_171-b11) (build 1.8.0_171-b11)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.171-b11 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V [libjvm.so+0x418bd4] ciEnv::get_field_by_index(ciInstanceKlass*, int)+0x94
#
# Core dump written. Default location: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/core or core.140400
#
# An error report file with more information is saved as:
# /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/hs_err_pid140400.log
[thread 140528350996224 also had an error]
# [ timer expired, abort... ]
Command completed. Elapsed time: 0:24:43. Running peak memory: 0.338GB.
PID: 140400; Command: fastqc; Return code: -6; Memory used: 0.338GB
Subprocess returned nonzero result. Check above output for details
ERROR: Subprocess returned nonzero result, but pipeline is continuing because nofail=True
> `FastQC report r1` fastqc/K562_PRO-seq_90_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/processed_R1.flag` (143002)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.338GB.
PID: 143002; Command: touch; Return code: 0; Memory used: 0.002GB
### Plot adapter insertion distribution (06-11 19:36:00) elapsed: 1696.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/cutadapt/K562_PRO-seq_90_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_PRO-seq_90/cutadapt/K562_PRO-seq_90_R1_cutadapt.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/cutadapt` (143009)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.338GB.
PID: 143009; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `Adapter insertion distribution` cutadapt/K562_PRO-seq_90_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_PRO-seq_90_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_PRO-seq_90/cutadapt/K562_PRO-seq_90_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` 34 PEPPRO _RES_
Missing stat 'Degradation_ratio'
### Calculating degradation ratio (06-11 19:36:05) elapsed: 5.0 _TIME_
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/cutadapt/K562_PRO-seq_90_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_PRO-seq_90/cutadapt/K562_PRO-seq_90_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_PRO-seq_90/cutadapt/K562_PRO-seq_90_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_PRO-seq_90/cutadapt/K562_PRO-seq_90_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_PRO-seq_90/cutadapt/K562_PRO-seq_90_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` 0.2312 PEPPRO _RES_
### Prealignments (06-11 19:36:05) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-11 19:36:05) elapsed: 0.0 _TIME_
> `(bowtie2 -p 32 -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_PRO-seq_90 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/prealignments/K562_PRO-seq_90_human_rDNA_unmap.fq 2>&1 > /dev/null)`
Missing stat 'Aligned_reads_human_rDNA'
435735817 reads; of these:
435735817 (100.00%) were unpaired; of these:
395519700 (90.77%) aligned 0 times
40216117 (9.23%) aligned exactly 1 time
0 (0.00%) aligned >1 times
9.23% overall alignment rate
> `Aligned_reads_human_rDNA` 40216117.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 9.23 PEPPRO _RES_
### Map to genome (06-11 20:34:47) elapsed: 3522.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam`
> `bowtie2 -p 32 --very-sensitive --rg-id K562_PRO-seq_90 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/prealignments/K562_PRO-seq_90_human_rDNA_unmap.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/tmpudv7sduc -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_temp.bam` (150325,150331,150332)
395519700 reads; of these:
395519700 (100.00%) were unpaired; of these:
4854399 (1.23%) aligned 0 times
295342485 (74.67%) aligned exactly 1 time
95322816 (24.10%) aligned >1 times
98.77% overall alignment rate
[bam_sort_core] merging from 127 files and 1 in-memory blocks...
Command completed. Elapsed time: 2:58:55. Running peak memory: 4.207GB.
PID: 150325; Command: bowtie2; Return code: 0; Memory used: 4.207GB
PID: 150331; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 150332; Command: samtools; Return code: 0; Memory used: 0.939GB
> `samtools view -q 10 -b -@ 32 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam` (172122)
Command completed. Elapsed time: 0:07:58. Running peak memory: 4.207GB.
PID: 172122; Command: samtools; Return code: 0; Memory used: 0.041GB
> `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_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 390665301 PEPPRO _RES_
> `QC_filtered_reads` 42066109 PEPPRO _RES_
> `Aligned_reads` 348599192 PEPPRO _RES_
> `Alignment_rate` 80.0 PEPPRO _RES_
> `Total_efficiency` 78.0 PEPPRO _RES_
> `Read_depth` 26.92 PEPPRO _RES_
### Compress all unmapped read files (06-12 00:34:39) elapsed: 14392.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/prealignments/K562_PRO-seq_90_human_rDNA_unmap.fq.gz`
> `pigz -f -p 32 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/prealignments/K562_PRO-seq_90_human_rDNA_unmap.fq` (178496)
Command completed. Elapsed time: 0:05:42. Running peak memory: 4.207GB.
PID: 178496; Command: pigz; Return code: 0; Memory used: 0.022GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_temp.bam` (179314)
Command completed. Elapsed time: 0:05:41. Running peak memory: 4.207GB.
PID: 179314; Command: samtools; Return code: 0; Memory used: 0.025GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 8235203 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam` (179863)
Command completed. Elapsed time: 0:05:05. Running peak memory: 4.207GB.
PID: 179863; Command: samtools; Return code: 0; Memory used: 0.025GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_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_PRO-seq_90/aligned_hg38/chr_sizes.bed` (180400,180401,180402,180403)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.207GB.
PID: 180402; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 180400; Command: samtools; Return code: 0; Memory used: 0.009GB
PID: 180403; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 180401; Command: cut; Return code: 0; Memory used: 0.001GB
> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/chr_sizes.bed -b -@ 32 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_noMT.bam` (180405)
Command completed. Elapsed time: 0:03:43. Running peak memory: 4.207GB.
PID: 180405; Command: samtools; Return code: 0; Memory used: 0.038GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam` (180666)
Command completed. Elapsed time: 0:00:03. Running peak memory: 4.207GB.
PID: 180666; Command: mv; Return code: 0; Memory used: 0.002GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam` (180671)
Command completed. Elapsed time: 0:05:02. Running peak memory: 4.207GB.
PID: 180671; Command: samtools; Return code: 0; Memory used: 0.025GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-`
> `Maximum_read_length` 100 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 (06-12 01:15:01) elapsed: 2422.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam.bai`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_bamQC.tsv`
> `/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam -c 32 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_bamQC.tsv` (182809)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/tmp_K562_PRO-seq_90_sort_56chre0b'
Processing with 32 cores...
Discarding 81 chunk(s) of reads: ['chrM', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270593v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', '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_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1']
Keeping 114 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_KI270710v1_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_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270310v1', 'chrUn_KI270411v1', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270515v1', 'chrUn_KI270538v1', 'chrUn_KI270583v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Command completed. Elapsed time: 0:03:39. Running peak memory: 13.68GB.
PID: 182809; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 13.68GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_bamQC.tsv`
> `NRF` 0.31 PEPPRO _RES_
> `PBC1` 0.57 PEPPRO _RES_
> `PBC2` 4.0 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_unmap.bam`
> `samtools view -b -@ 32 -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_unmap.bam` (183291)
Command completed. Elapsed time: 0:01:35. Running peak memory: 13.68GB.
PID: 183291; Command: samtools; Return code: 0; Memory used: 0.017GB
> `samtools view -c -f 4 -@ 32 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_temp.bam`
> `Unmapped_reads` 4854399 PEPPRO _RES_
### Split BAM by strand (06-12 01:21:17) elapsed: 377.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam` (183755)
Command completed. Elapsed time: 0:24:56. Running peak memory: 13.68GB.
PID: 183755; 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_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam` (186344)
Command completed. Elapsed time: 0:22:55. Running peak memory: 13.68GB.
PID: 186344; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-12 02:09:09) elapsed: 2871.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (188644)
Command completed. Elapsed time: 0:00:00. Running peak memory: 13.68GB.
PID: 188644; Command: sed; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_plus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/plus_TSS.tsv -p ends -c 32 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_plus_TssEnrichment.txt` (188650)
Command completed. Elapsed time: 0:00:30. Running peak memory: 13.68GB.
PID: 188650; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 2.008GB
> `TSS_coding_score` 13.9 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_minus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/minus_TSS.tsv -p ends -c 32 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_minus_TssEnrichment.txt` (188746)
Command completed. Elapsed time: 0:00:25. Running peak memory: 13.68GB.
PID: 188746; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 2.25GB
> `TSS_non-coding_score` 5.8 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_TSSenrichment.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_minus_TssEnrichment.txt` (189078)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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: 0:00:07. Running peak memory: 13.68GB.
PID: 189078; Command: Rscript; Return code: 0; Memory used: 0.257GB
> `TSS enrichment` QC_hg38/K562_PRO-seq_90_TSSenrichment.pdf TSS enrichment QC_hg38/K562_PRO-seq_90_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_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_PRO-seq_90/QC_hg38/chr_order.txt` (189110,189111,189112,189113)
Command completed. Elapsed time: 0:00:00. Running peak memory: 13.68GB.
PID: 189110; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 189112; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 189111; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 189113; Command: awk; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_keep.txt` (189119)
Command completed. Elapsed time: 0:00:00. Running peak memory: 13.68GB.
PID: 189119; Command: cut; Return code: 0; Memory used: 0.002GB
### Calculate Pause Index (PI) (06-12 02:10:11) elapsed: 63.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/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_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_ensembl_tss.bed` (189121,189122)
Command completed. Elapsed time: 0:00:02. Running peak memory: 13.68GB.
PID: 189121; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 189122; Command: bedtools; Return code: 0; Memory used: 0.048GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/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_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_ensembl_gene_body.bed` (189126,189127)
Command completed. Elapsed time: 0:00:00. Running peak memory: 13.68GB.
PID: 189126; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 189127; Command: bedtools; Return code: 0; Memory used: 0.022GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/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_PRO-seq_90/QC_hg38/K562_PRO-seq_90_TSS_density.bed` (189129,189130,189131,189132)
Command completed. Elapsed time: 0:07:26. Running peak memory: 13.68GB.
PID: 189131; Command: sort; Return code: 0; Memory used: 0.01GB
PID: 189129; Command: bedtools; Return code: 0; Memory used: 0.094GB
PID: 189132; Command: sort; Return code: 0; Memory used: 0.003GB
PID: 189130; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_gene_body_density.bed` (189770,189776,189777)
Command completed. Elapsed time: 0:12:17. Running peak memory: 13.68GB.
PID: 189776; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 189770; Command: bedtools; Return code: 0; Memory used: 0.922GB
PID: 189777; Command: sort; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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_PRO-seq_90/QC_hg38/K562_PRO-seq_90_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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_PRO-seq_90/QC_hg38/tmp1z2_cdzc` (190955,190960,190961)
Command completed. Elapsed time: 0:00:01. Running peak memory: 13.68GB.
PID: 190955; Command: join; Return code: 0; Memory used: 0.001GB
PID: 190961; Command: env; Return code: 0; Memory used: 0.006GB
PID: 190960; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/tmp1z2_cdzc | 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: (06-12 02:29:58) elapsed: 1186.0 _TIME_
Total time: 7:22:17
Failure reason: Command 'awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/tmp1z2_cdzc | 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_PRO-seq_90 --genome hg38 --input /project/shefflab/data//guertin/fastq/K562_PRO_90pct.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 32 -M 32000 --protocol PRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-aj37-15c1
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/
* Pipeline started at: (06-14 21:10:54) elapsed: 6.0 _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`: `32`
* `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//guertin/fastq/K562_PRO_90pct.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `32000`
* `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`: `PRO`
* `recover`: `True`
* `sample_name`: `K562_PRO-seq_90`
* `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_PRO-seq_90/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//guertin/fastq/K562_PRO_90pct.fastq.gz
> `File_mb` 32665.2 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-14 21:10:55) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz'
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/K562_PRO-seq_90_R1.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/K562_PRO-seq_90.fastq.gz']
### FASTQ processing: (06-14 21:10:55) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/fastq/processed_R1.flag`
### Plot adapter insertion distribution (06-14 21:10:55) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/cutadapt/K562_PRO-seq_90_R1_adapter_insertion_distribution.pdf`
> `Adapter insertion distribution` cutadapt/K562_PRO-seq_90_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_PRO-seq_90_R1_adapter_insertion_distribution.png PEPPRO _OBJ_
### Prealignments (06-14 21:10:55) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-14 21:10:55) elapsed: 0.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/prealignments/K562_PRO-seq_90_human_rDNA_unmap.fq
### Map to genome (06-14 21:10:55) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam`
### Compress all unmapped read files (06-14 21:10:55) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/prealignments/K562_PRO-seq_90_human_rDNA_unmap.fq.gz`
### Calculate NRF, PBC1, and PBC2 (06-14 21:10:55) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam.bai`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_bamQC.tsv`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_unmap.bam`
### Split BAM by strand (06-14 21:10:55) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam`
### Calculate TSS enrichment (06-14 21:10:55) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_TSSenrichment.pdf`
> `TSS enrichment` QC_hg38/K562_PRO-seq_90_TSSenrichment.pdf TSS enrichment QC_hg38/K562_PRO-seq_90_TSSenrichment.png PEPPRO _OBJ_
### Calculate Pause Index (PI) (06-14 21:10:55) elapsed: 0.0 _TIME_
Missing stat 'Pause_index'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_ensembl_tss.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_ensembl_gene_body.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_TSS_density.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_gene_body_density.bed`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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_PRO-seq_90/QC_hg38/K562_PRO-seq_90_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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_PRO-seq_90/QC_hg38/tmpv8d2cgo6` (91080,91081,91082)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.006GB.
PID: 91080; Command: join; Return code: 0; Memory used: 0.001GB
PID: 91082; Command: env; Return code: 0; Memory used: 0.006GB
PID: 91081; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/tmpv8d2cgo6 | 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_PRO-seq_90/QC_hg38/K562_PRO-seq_90_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.191125) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/tmpv8d2cgo6 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_pause_index.bed` (91090)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.006GB.
PID: 91090; Command: awk; Return code: 0; Memory used: 0.004GB
> `sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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` 10.94 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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_PRO-seq_90/QC_hg38/K562_PRO-seq_90_pause_index.bed` (91095)
Pause index plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.287GB.
PID: 91095; Command: Rscript; Return code: 0; Memory used: 0.287GB
> `Pause index` QC_hg38/K562_PRO-seq_90_pause_index.pdf Pause index QC_hg38/K562_PRO-seq_90_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_pause_index.bed.gz`
> `pigz -f -p 32 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_pause_index.bed` (91129)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.287GB.
PID: 91129; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-14 21:11:01) 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_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam`
348599192 124340900
> `Plus_FRiP` 0.36 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_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam`
348599192 118257966
> `Minus_FRiP` 0.34 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/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_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_gene_sort.bed` (180177,180178)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.287GB.
PID: 180177; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 180178; Command: bedtools; Return code: 0; Memory used: 0.004GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_gene_coverage.bed` (180181)
Command completed. Elapsed time: 0:12:47. Running peak memory: 0.923GB.
PID: 180181; Command: bedtools; Return code: 0; Memory used: 0.923GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/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_PRO-seq_90/raw/hg38_annotations.bed.gz` (313421)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.923GB.
PID: 313421; Command: ln; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 32 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/hg38_annotations.bed` (313426)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.923GB.
PID: 313426; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-14 21:33:45) elapsed: 1363.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/raw/hg38_annotations.bed` (313435)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.923GB.
PID: 313435; Command: awk; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Enhancer_sort.bed` (313437,313438,313439,313440)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.923GB.
PID: 313437; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 313438; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 313440; Command: bedtools; Return code: 0; Memory used: 0.047GB
PID: 313439; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Enhancer_plus_coverage.bed` (313442)
Command completed. Elapsed time: 0:03:48. Running peak memory: 0.923GB.
PID: 313442; Command: bedtools; Return code: 0; Memory used: 0.034GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Enhancer_minus_coverage.bed` (313896)
Command completed. Elapsed time: 0:03:47. Running peak memory: 0.923GB.
PID: 313896; Command: bedtools; Return code: 0; Memory used: 0.063GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_sort.bed` (314358,314359,314360,314361)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.923GB.
PID: 314358; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 314359; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 314361; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 314360; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_plus_coverage.bed` (314363)
Command completed. Elapsed time: 0:04:03. Running peak memory: 0.923GB.
PID: 314363; Command: bedtools; Return code: 0; Memory used: 0.532GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_minus_coverage.bed` (314799)
Command completed. Elapsed time: 0:04:01. Running peak memory: 0.923GB.
PID: 314799; Command: bedtools; Return code: 0; Memory used: 0.426GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_Flanking_Region"` (315041)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.923GB.
PID: 315041; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/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_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed` (315043,315044,315045,315046)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.923GB.
PID: 315043; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 315045; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 315044; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 315046; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_Flanking_Region_plus_coverage.bed` (315049)
Command completed. Elapsed time: 0:03:43. Running peak memory: 0.923GB.
PID: 315049; Command: bedtools; Return code: 0; Memory used: 0.089GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_Flanking_Region_minus_coverage.bed` (315514)
Command completed. Elapsed time: 0:03:38. Running peak memory: 0.923GB.
PID: 315514; Command: bedtools; Return code: 0; Memory used: 0.15GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/5_UTR"` (315921)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.923GB.
PID: 315921; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/5_UTR_sort.bed` (315922,315923,315924,315925)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.923GB.
PID: 315922; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 315923; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 315925; Command: bedtools; Return code: 0; Memory used: 0.03GB
PID: 315924; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_5_UTR_plus_coverage.bed` (315928)
Command completed. Elapsed time: 0:03:40. Running peak memory: 0.923GB.
PID: 315928; Command: bedtools; Return code: 0; Memory used: 0.069GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_5_UTR_minus_coverage.bed` (316396)
Command completed. Elapsed time: 0:03:29. Running peak memory: 0.923GB.
PID: 316396; Command: bedtools; Return code: 0; Memory used: 0.044GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/3_UTR"` (316621)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.923GB.
PID: 316621; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/3_UTR_sort.bed` (316622,316623,316624,316625)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.923GB.
PID: 316622; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 316623; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 316625; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 316624; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_3_UTR_plus_coverage.bed` (316627)
Command completed. Elapsed time: 0:03:41. Running peak memory: 0.923GB.
PID: 316627; Command: bedtools; Return code: 0; Memory used: 0.094GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_3_UTR_minus_coverage.bed` (317072)
Command completed. Elapsed time: 0:03:41. Running peak memory: 0.923GB.
PID: 317072; Command: bedtools; Return code: 0; Memory used: 0.146GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Exon_sort.bed` (361533,361534,361535,361536)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.923GB.
PID: 361533; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 361534; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 361536; Command: bedtools; Return code: 0; Memory used: 0.173GB
PID: 361535; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Exon_plus_coverage.bed` (361541)
Command completed. Elapsed time: 0:03:59. Running peak memory: 0.923GB.
PID: 361541; Command: bedtools; Return code: 0; Memory used: 0.422GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Exon_minus_coverage.bed` (362015)
Command completed. Elapsed time: 0:03:52. Running peak memory: 0.923GB.
PID: 362015; Command: bedtools; Return code: 0; Memory used: 0.169GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Intron_sort.bed` (362250,362251,362252,362253)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.923GB.
PID: 362250; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 362252; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 362251; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 362253; Command: bedtools; Return code: 0; Memory used: 0.084GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Intron_plus_coverage.bed` (362256)
Command completed. Elapsed time: 0:04:44. Running peak memory: 0.923GB.
PID: 362256; Command: bedtools; Return code: 0; Memory used: 0.409GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Intron_minus_coverage.bed` (394677)
Command completed. Elapsed time: 0:04:53. Running peak memory: 0.923GB.
PID: 394677; Command: bedtools; Return code: 0; Memory used: 0.393GB
### Plot cFRiF/FRiF (06-14 22:28:52) elapsed: 3307.0 _TIME_
> `samtools view -@ 32 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_PRO-seq_90 -z 3099922541 -n 173476883 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Intron_plus_coverage.bed` (451252)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:39. Running peak memory: 0.923GB.
PID: 451252; Command: Rscript; Return code: 0; Memory used: 0.445GB
> `cFRiF` QC_hg38/K562_PRO-seq_90_cFRiF.pdf cFRiF QC_hg38/K562_PRO-seq_90_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_PRO-seq_90 -z 3099922541 -n 173476883 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_Intron_plus_coverage.bed` (451310)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:26. Running peak memory: 0.923GB.
PID: 451310; Command: Rscript; Return code: 0; Memory used: 0.443GB
> `FRiF` QC_hg38/K562_PRO-seq_90_FRiF.pdf FRiF QC_hg38/K562_PRO-seq_90_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-14 22:30:24) elapsed: 92.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/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_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_exons_sort.bed` (451664,451665)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.923GB.
PID: 451664; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 451665; Command: bedtools; Return code: 0; Memory used: 0.099GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/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_PRO-seq_90/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_introns_sort.bed` (451671,451672,451673)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.923GB.
PID: 451671; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 451673; Command: bedtools; Return code: 0; Memory used: 0.006GB
PID: 451672; Command: bedtools; Return code: 0; Memory used: 0.036GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_exons_coverage.bed` (451690)
Command completed. Elapsed time: 0:08:05. Running peak memory: 0.923GB.
PID: 451690; Command: bedtools; Return code: 0; Memory used: 0.264GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_introns_coverage.bed` (82153)
Command completed. Elapsed time: 0:10:57. Running peak memory: 0.923GB.
PID: 82153; Command: bedtools; Return code: 0; Memory used: 0.439GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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]/348.599192)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_exons_rpkm.bed` (182289,182295,182296)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.923GB.
PID: 182289; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 182296; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 182295; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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]/348.599192)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_introns_rpkm.bed` (182298,182299,182300)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.923GB.
PID: 182298; Command: awk; Return code: 0; Memory used: 0.006GB
PID: 182300; Command: sort; Return code: 0; Memory used: 0.003GB
PID: 182299; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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_PRO-seq_90/QC_hg38/K562_PRO-seq_90_exon_intron_ratios.bed` (182302,182303,182304)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.923GB.
PID: 182302; Command: join; Return code: 0; Memory used: 0.001GB
PID: 182304; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 182303; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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` 1.37 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_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_PRO-seq_90/QC_hg38/K562_PRO-seq_90_exon_intron_ratios.bed --annotate` (182311)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.923GB.
PID: 182311; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `mRNA contamination` QC_hg38/K562_PRO-seq_90_mRNA_contamination.pdf mRNA contamination QC_hg38/K562_PRO-seq_90_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_exon_intron_ratios.bed.gz`
> `pigz -f -p 32 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/QC_hg38/K562_PRO-seq_90_exon_intron_ratios.bed` (182345)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.923GB.
PID: 182345; Command: pigz; Return code: 0; Memory used: 0.005GB
### Produce bigWig files (06-14 22:49:43) elapsed: 1159.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam` (182354)
Command completed. Elapsed time: 0:02:24. Running peak memory: 0.923GB.
PID: 182354; Command: samtools; Return code: 0; Memory used: 0.016GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_plus_smooth_body_0-mer.bw -p 21 --variable-step --tail-edge --scale 348599192.0` (183669)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_plus.bam'
Temporary files will be stored in: 'tmp_K562_PRO-seq_90_plus_cuttrace_igd3jtq2'
Processing with 10 cores...
stdin is empty of data
stdin is empty of data
Discarding 90 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_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_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270581v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', '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_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1']
Keeping 105 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_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270538v1', 'chrUn_KI270580v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 105 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_plus_exact_body_0-mer.bw'
Merging 105 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:08:03. Running peak memory: 4.138GB.
PID: 183669; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 4.138GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam` (272789)
Command completed. Elapsed time: 0:02:37. Running peak memory: 4.138GB.
PID: 272789; Command: samtools; Return code: 0; Memory used: 0.015GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_minus_smooth_body_0-mer.bw -p 21 --variable-step --tail-edge --scale 348599192.0` (316933)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/aligned_hg38/K562_PRO-seq_90_minus.bam'
Temporary files will be stored in: 'tmp_K562_PRO-seq_90_minus_cuttrace_m7dv06yi'
Processing with 10 cores...
stdin is empty of data
stdin is empty of data
stdin is empty of data
stdin is empty of data
stdin is empty of data
Discarding 94 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr9_KI270717v1_random', 'chr14_KI270723v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', '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_KI270511v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270593v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', '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_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1']
Keeping 101 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_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_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_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270310v1', 'chrUn_KI270411v1', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270515v1', 'chrUn_KI270538v1', 'chrUn_KI270583v1', 'chrUn_KI270581v1', 'chrUn_KI270589v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270336v1', 'chrUn_KI270448v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 101 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_minus_exact_body_0-mer.bw'
Merging 101 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_90/signal_hg38/K562_PRO-seq_90_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:07:44. Running peak memory: 4.671GB.
PID: 316933; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 4.671GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 1:59:42
* Total elapsed time (all runs): 12:14:11
* Peak memory (this run): 4.6705 GB
* Pipeline completed time: 2020-06-14 23:10:30