### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name Jurkat_ChRO-seq_1 --genome hg38 --input /project/shefflab/data//sra_fastq/SRR7616133.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol PRO --umi-len 6 --scale --prealignments human_rDNA --dirty`
* Compute host: udc-aj40-13c1
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/
* Pipeline started at: (06-11 17:35:31) elapsed: 1.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//sra_fastq/SRR7616133.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `12000`
* `new_start`: `False`
* `no_fifo`: `False`
* `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline`
* `paired_end`: `False`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `PRO`
* `recover`: `False`
* `sample_name`: `Jurkat_ChRO-seq_1`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `SINGLE`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `6`
* `verbosity`: `None`
----------------------------------------
Local input file: /project/shefflab/data//sra_fastq/SRR7616133.fastq.gz
> `File_mb` 1330.25 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-11 17:35:33) elapsed: 2.0 _TIME_
Number of input file sets: 1
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz`
> `ln -sf /project/shefflab/data//sra_fastq/SRR7616133.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz` (26733)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 26733; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz'
Found .fastq.gz file
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1.fastq`
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1.fastq` (26734)
Command completed. Elapsed time: 0:00:53. Running peak memory: 0.002GB.
PID: 26734; Command: pigz; Return code: 0; Memory used: 0.002GB
> `Raw_reads` 37740511 PEPPRO _RES_
> `Fastq_reads` 37740511 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz']
### FASTQ processing: (06-11 17:36:47) elapsed: 74.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_processed.fastq`
> `(cutadapt -j 12 -m 8 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_R1_cutadapt.txt` (26828)
Command completed. Elapsed time: 0:00:45. Running peak memory: 2.039GB.
PID: 26828; Command: cutadapt; Return code: 0; Memory used: 2.039GB
> `seqtk trimfq -b 6 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_noadap.fastq | seqtk seq -L 8 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_processed.fastq` (26904,26905)
Command completed. Elapsed time: 0:00:38. Running peak memory: 2.039GB.
PID: 26904; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 26905; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 32783879 PEPPRO _RES_
> `Trim_loss_rate` 13.13 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_processed.fastq` (26963)
Started analysis of Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 5% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 10% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 15% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 20% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 25% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 30% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 35% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 40% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 45% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 50% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 55% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 60% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 65% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 70% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 75% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 80% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 85% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 90% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Approx 95% complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Analysis complete for Jurkat_ChRO-seq_1_R1_processed.fastq
Command completed. Elapsed time: 0:01:06. Running peak memory: 2.039GB.
PID: 26963; Command: fastqc; Return code: 0; Memory used: 0.176GB
> `FastQC report r1` fastqc/Jurkat_ChRO-seq_1_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_trimmed.fastq`
> `seqkit rmdup --threads 12 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_noadap.fastq` (27048)
[INFO][0m 14846147 duplicated records removed
Command completed. Elapsed time: 0:00:41. Running peak memory: 2.039GB.
PID: 27048; Command: seqkit; Return code: 0; Memory used: 1.036GB
> `seqtk trimfq -b 6 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_dedup.fastq | seqtk seq -L 8 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_trimmed.fastq` (27369,27370)
Command completed. Elapsed time: 0:00:21. Running peak memory: 2.039GB.
PID: 27369; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 27370; Command: seqtk; Return code: 0; Memory used: 0.002GB
> `grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 34473620.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 2012355.0 PEPPRO _RES_
> `Duplicate_reads` 14846147.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 5.3321 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/processed_R1.flag` (27478)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.039GB.
PID: 27478; Command: touch; Return code: 0; Memory used: 0.002GB
### Plot adapter insertion distribution (06-11 17:41:41) elapsed: 293.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_R1_cutadapt.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/cutadapt -u 6` (27479)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:12. Running peak memory: 2.039GB.
PID: 27479; Command: Rscript; Return code: 0; Memory used: 0.108GB
> `Adapter insertion distribution` cutadapt/Jurkat_ChRO-seq_1_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_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` 20 PEPPRO _RES_
Missing stat 'Degradation_ratio'
### Calculating degradation ratio (06-11 17:41:52) elapsed: 12.0 _TIME_
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_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` 0.9566 PEPPRO _RES_
### Prealignments (06-11 17:41:53) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-11 17:41:53) elapsed: 0.0 _TIME_
> `(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id Jurkat_ChRO-seq_1 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap.fq 2>&1 > /dev/null)`
Missing stat 'Aligned_reads_human_rDNA'
32783879 reads; of these:
32783879 (100.00%) were unpaired; of these:
29290636 (89.34%) aligned 0 times
3493243 (10.66%) aligned exactly 1 time
0 (0.00%) aligned >1 times
10.66% overall alignment rate
> `Aligned_reads_human_rDNA` 3493243.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 10.66 PEPPRO _RES_
### Map to human_rDNA (06-11 17:44:54) elapsed: 181.0 _TIME_
> `(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id Jurkat_ChRO-seq_1 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap_dups.fq 2>&1 > /dev/null)`
### Map to genome (06-11 17:46:43) elapsed: 109.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_fail_qc_dups.bam
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam`
> `bowtie2 -p 12 --very-sensitive --rg-id Jurkat_ChRO-seq_1 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/tmpgdqhj09o -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp.bam` (28061,28062,28063)
29290636 reads; of these:
29290636 (100.00%) were unpaired; of these:
1113286 (3.80%) aligned 0 times
17309978 (59.10%) aligned exactly 1 time
10867372 (37.10%) aligned >1 times
96.20% overall alignment rate
[bam_sort_core] merging from 8 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:11:07. Running peak memory: 3.685GB.
PID: 28061; Command: bowtie2; Return code: 0; Memory used: 3.685GB
PID: 28062; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 28063; Command: samtools; Return code: 0; Memory used: 0.9GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam` (3548)
Command completed. Elapsed time: 0:00:51. Running peak memory: 3.685GB.
PID: 3548; Command: samtools; Return code: 0; Memory used: 0.018GB
> `samtools depth -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 28177350 PEPPRO _RES_
> `QC_filtered_reads` 6839271 PEPPRO _RES_
> `Aligned_reads` 21338079 PEPPRO _RES_
> `Alignment_rate` 65.09 PEPPRO _RES_
> `Total_efficiency` 56.54 PEPPRO _RES_
> `Read_depth` 3.87 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort_dups.bam`
> `bowtie2 -p 12 --very-sensitive --rg-id Jurkat_ChRO-seq_1 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap_dups.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/tmpgdqhj09o -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp_dups.bam` (4698,4703,4704)
18024676 reads; of these:
18024676 (100.00%) were unpaired; of these:
856458 (4.75%) aligned 0 times
10720803 (59.48%) aligned exactly 1 time
6447415 (35.77%) aligned >1 times
95.25% overall alignment rate
[bam_sort_core] merging from 5 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:07:33. Running peak memory: 3.685GB.
PID: 4698; Command: bowtie2; Return code: 0; Memory used: 3.684GB
PID: 4703; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 4704; Command: samtools; Return code: 0; Memory used: 0.899GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort_dups.bam` (5505)
Command completed. Elapsed time: 0:00:35. Running peak memory: 3.685GB.
PID: 5505; Command: samtools; Return code: 0; Memory used: 0.018GB
### Compress all unmapped read files (06-11 18:14:58) elapsed: 1695.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap.fq` (5562)
Command completed. Elapsed time: 0:00:36. Running peak memory: 3.685GB.
PID: 5562; Command: pigz; Return code: 0; Memory used: 0.011GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp.bam` (5831)
Command completed. Elapsed time: 0:00:20. Running peak memory: 3.685GB.
PID: 5831; Command: samtools; Return code: 0; Memory used: 0.015GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 4738 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam` (5859)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.685GB.
PID: 5859; Command: samtools; Return code: 0; Memory used: 0.015GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/aligned_hg38/chr_sizes.bed` (5883,5884,5885,5886)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.685GB.
PID: 5883; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 5885; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 5884; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 5886; Command: grep; Return code: 0; Memory used: 0.0GB
> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_noMT.bam` (5888)
Command completed. Elapsed time: 0:00:19. Running peak memory: 3.685GB.
PID: 5888; Command: samtools; Return code: 0; Memory used: 0.018GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam` (5926)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.685GB.
PID: 5926; Command: mv; Return code: 0; Memory used: 0.002GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam` (5927)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.685GB.
PID: 5927; Command: samtools; Return code: 0; Memory used: 0.015GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-`
> `Maximum_read_length` 70 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_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp_dups.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp_dups.bam` (6012)
Command completed. Elapsed time: 0:00:13. Running peak memory: 3.685GB.
PID: 6012; Command: samtools; Return code: 0; Memory used: 0.009GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp_dups.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort_dups.bam`
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort_dups.bam.bai
### Calculate library complexity (06-11 18:17:51) elapsed: 173.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_out.txt`
> `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort_dups.bam` (6027)
BAM_INPUT
TOTAL READS = 13139331
COUNTS_SUM = 13139331
DISTINCT READS = 9.95264e+06
DISTINCT COUNTS = 149
MAX COUNT = 430
COUNTS OF 1 = 8.33143e+06
OBSERVED COUNTS (431)
1 8331431
2 1064073
3 273280
4 110730
5 57100
6 33562
7 21886
8 14351
9 10164
10 7277
11 5449
12 4060
13 3259
14 2572
15 2117
16 1690
17 1348
18 1122
19 924
20 809
21 697
22 515
23 473
24 408
25 362
26 314
27 268
28 197
29 186
30 150
31 147
32 163
33 117
34 133
35 90
36 92
37 78
38 88
39 59
40 50
41 60
42 49
43 34
44 46
45 41
46 32
47 44
48 36
49 27
50 22
51 33
52 22
53 21
54 16
55 20
56 17
57 20
58 12
59 14
60 10
61 9
62 8
63 12
64 9
65 11
66 6
67 8
68 5
69 10
70 8
71 8
72 7
73 3
74 8
75 3
76 6
77 5
78 2
79 3
80 6
81 5
82 6
83 7
84 3
85 4
86 2
87 2
88 3
89 3
90 4
91 2
92 6
93 2
94 4
95 3
96 2
98 1
99 2
100 2
101 1
102 3
104 1
105 1
107 2
108 2
109 1
110 5
111 2
112 1
113 1
114 1
116 2
117 2
118 2
123 1
125 1
126 1
128 1
132 1
133 2
134 1
135 1
136 1
139 1
141 1
143 1
144 1
147 2
150 1
151 1
156 2
167 2
168 1
172 2
174 1
177 1
189 1
191 1
193 2
215 1
216 1
225 1
280 1
296 1
349 1
361 1
388 1
402 1
430 1
sample size: 1000000
sample size: 2000000
sample size: 3000000
sample size: 4000000
sample size: 5000000
sample size: 6000000
sample size: 7000000
sample size: 8000000
sample size: 9000000
sample size: 10000000
sample size: 11000000
sample size: 12000000
sample size: 13000000
Command completed. Elapsed time: 0:01:12. Running peak memory: 3.685GB.
PID: 6027; Command: preseq; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_yield.txt`
> `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort_dups.bam` (6135)
BAM_INPUT
TOTAL READS = 13139331
DISTINCT READS = 9.95264e+06
DISTINCT COUNTS = 149
MAX COUNT = 430
COUNTS OF 1 = 8.33143e+06
MAX TERMS = 96
OBSERVED COUNTS (431)
1 8331431
2 1064073
3 273280
4 110730
5 57100
6 33562
7 21886
8 14351
9 10164
10 7277
11 5449
12 4060
13 3259
14 2572
15 2117
16 1690
17 1348
18 1122
19 924
20 809
21 697
22 515
23 473
24 408
25 362
26 314
27 268
28 197
29 186
30 150
31 147
32 163
33 117
34 133
35 90
36 92
37 78
38 88
39 59
40 50
41 60
42 49
43 34
44 46
45 41
46 32
47 44
48 36
49 27
50 22
51 33
52 22
53 21
54 16
55 20
56 17
57 20
58 12
59 14
60 10
61 9
62 8
63 12
64 9
65 11
66 6
67 8
68 5
69 10
70 8
71 8
72 7
73 3
74 8
75 3
76 6
77 5
78 2
79 3
80 6
81 5
82 6
83 7
84 3
85 4
86 2
87 2
88 3
89 3
90 4
91 2
92 6
93 2
94 4
95 3
96 2
98 1
99 2
100 2
101 1
102 3
104 1
105 1
107 2
108 2
109 1
110 5
111 2
112 1
113 1
114 1
116 2
117 2
118 2
123 1
125 1
126 1
128 1
132 1
133 2
134 1
135 1
136 1
139 1
141 1
143 1
144 1
147 2
150 1
151 1
156 2
167 2
168 1
172 2
174 1
177 1
189 1
191 1
193 2
215 1
216 1
225 1
280 1
296 1
349 1
361 1
388 1
402 1
430 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
.................._...._..............................................................................
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]
Command completed. Elapsed time: 0:01:13. Running peak memory: 3.685GB.
PID: 6135; Command: preseq; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_counts.txt`
> `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort_dups.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_counts.txt` (6527)
Command completed. Elapsed time: 0:00:22. Running peak memory: 3.685GB.
PID: 6527; Command: echo; Return code: 0; Memory used: 0.006GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_plot.png`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R preseq -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_plot` (6549)
Processing Jurkat_ChRO-seq_1
INFO: Found real counts for Jurkat_ChRO-seq_1 - Total (M): 21.334642 Unique (M): 13.139331
Library complexity plot completed!
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.685GB.
PID: 6549; Command: Rscript; Return code: 0; Memory used: 0.085GB
> `Library complexity` QC_hg38/Jurkat_ChRO-seq_1_preseq_plot.pdf Library complexity QC_hg38/Jurkat_ChRO-seq_1_preseq_plot.png PEPPRO _OBJ_
Missing stat 'Frac_exp_unique_at_10M'
> `grep -w '10000000' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_preseq_yield.txt | awk '{print $2}'`
> `Frac_exp_unique_at_10M` 0.7897 PEPPRO _RES_
### Calculate NRF, PBC1, and PBC2 (06-11 18:20:51) elapsed: 180.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam.bai`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_bamQC.tsv`
> `/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_bamQC.tsv` (6575)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/tmp_Jurkat_ChRO-seq_1_sort_qn69eg_r'
Processing with 12 cores...
Discarding 109 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr9_KI270717v1_random', 'chr22_KI270732v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270581v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1']
Keeping 86 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_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_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_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chrUn_KI270442v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270538v1', 'chrUn_KI270583v1', 'chrUn_KI270580v1', 'chrUn_KI270579v1', 'chrUn_KI270330v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Command completed. Elapsed time: 0:00:23. Running peak memory: 3.685GB.
PID: 6575; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.521GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_bamQC.tsv`
> `NRF` 0.38 PEPPRO _RES_
> `PBC1` 0.64 PEPPRO _RES_
> `PBC2` 3.39 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_unmap.bam`
> `samtools view -b -@ 12 -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_unmap.bam` (6641)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.685GB.
PID: 6641; Command: samtools; Return code: 0; Memory used: 0.009GB
> `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_temp.bam`
> `Unmapped_reads` 1113286 PEPPRO _RES_
### Split BAM by strand (06-11 18:21:24) elapsed: 33.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam` (6680)
Command completed. Elapsed time: 0:01:00. Running peak memory: 3.685GB.
PID: 6680; Command: samtools; Return code: 0; Memory used: 0.006GB
> `samtools view -bh -f 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam` (6747)
Command completed. Elapsed time: 0:00:59. Running peak memory: 3.685GB.
PID: 6747; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-11 18:23:23) elapsed: 119.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (6824)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.685GB.
PID: 6824; Command: sed; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_plus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_plus_TssEnrichment.txt` (6825)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.685GB.
PID: 6825; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.534GB
> `TSS_coding_score` 55.1 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_minus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_minus_TssEnrichment.txt` (6860)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.685GB.
PID: 6860; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.726GB
> `TSS_non-coding_score` 12.6 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSSenrichment.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_minus_TssEnrichment.txt` (6893)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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: 0:00:11. Running peak memory: 3.685GB.
PID: 6893; Command: Rscript; Return code: 0; Memory used: 0.108GB
> `TSS enrichment` QC_hg38/Jurkat_ChRO-seq_1_TSSenrichment.pdf TSS enrichment QC_hg38/Jurkat_ChRO-seq_1_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt` (6919,6920,6921,6922)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.685GB.
PID: 6919; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 6921; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 6920; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 6922; Command: awk; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_keep.txt` (6924)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.685GB.
PID: 6924; Command: cut; Return code: 0; Memory used: 0.002GB
### Calculate Pause Index (PI) (06-11 18:23:49) elapsed: 26.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/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/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_tss.bed` (6926,6927)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.685GB.
PID: 6926; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 6927; Command: bedtools; Return code: 0; Memory used: 0.093GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/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/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_gene_body.bed` (6931,6932)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.685GB.
PID: 6931; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 6932; Command: bedtools; Return code: 0; Memory used: 0.004GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/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/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSS_density.bed` (6934,6935,6936,6937)
Command completed. Elapsed time: 0:00:26. Running peak memory: 3.685GB.
PID: 6935; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 6937; Command: sort; Return code: 0; Memory used: 0.002GB
PID: 6934; Command: bedtools; Return code: 0; Memory used: 0.027GB
PID: 6936; Command: sort; Return code: 0; Memory used: 0.004GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_gene_body_density.bed` (6977,6978,6979)
Command completed. Elapsed time: 0:00:33. Running peak memory: 3.685GB.
PID: 6979; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 6977; Command: bedtools; Return code: 0; Memory used: 0.099GB
PID: 6978; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_pause_index.bed`
awk: cmd. line:1: { if ($5 == ){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}
awk: cmd. line:1: ^ syntax error
awk: cmd. line:1: { if ($5 == ){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}
awk: cmd. line:1: ^ syntax error
> `join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/QC_hg38/tmpf89gr92g` (7009,7010,7011)
Got SIGTERM. Failing gracefully... (06-11 18:55:14) elapsed: 1885.0 _TIME_
Child process 7009 (join) terminated after 0 sec.
Setting dynamic recover file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/recover.lock.QC_hg38__Jurkat_ChRO-seq_1_pause_index.bed
### Pipeline failed at: (06-11 18:55:14) elapsed: 0.0 _TIME_
Total time: 1:19:45
Failure reason: SIGTERM
Pipeline aborted.
### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name Jurkat_ChRO-seq_1 --genome hg38 --input /project/shefflab/data//sra_fastq/SRR7616133.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol PRO --umi-len 6 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba26-12
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/
* Pipeline started at: (06-11 19:11:35) elapsed: 0.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//sra_fastq/SRR7616133.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `12000`
* `new_start`: `False`
* `no_fifo`: `False`
* `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline`
* `paired_end`: `False`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `PRO`
* `recover`: `True`
* `sample_name`: `Jurkat_ChRO-seq_1`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `SINGLE`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `6`
* `verbosity`: `None`
----------------------------------------
Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//sra_fastq/SRR7616133.fastq.gz
> `File_mb` 1330.25 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-11 19:11:36) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz'
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz']
### FASTQ processing: (06-11 19:11:36) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/processed_R1.flag`
### Plot adapter insertion distribution (06-11 19:11:36) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_R1_adapter_insertion_distribution.pdf`
> `Adapter insertion distribution` cutadapt/Jurkat_ChRO-seq_1_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/Jurkat_ChRO-seq_1_R1_adapter_insertion_distribution.png PEPPRO _OBJ_
### Prealignments (06-11 19:11:36) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-11 19:11:36) elapsed: 0.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap.fq
### Map to human_rDNA (06-11 19:11:36) elapsed: 0.0 _TIME_
### Map to genome (06-11 19:11:36) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam`
### Compress all unmapped read files (06-11 19:11:36) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap.fq.gz`
### Calculate NRF, PBC1, and PBC2 (06-11 19:11:36) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam.bai`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_bamQC.tsv`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_unmap.bam`
### Split BAM by strand (06-11 19:11:36) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam`
### Calculate TSS enrichment (06-11 19:11:36) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSSenrichment.pdf`
> `TSS enrichment` QC_hg38/Jurkat_ChRO-seq_1_TSSenrichment.pdf TSS enrichment QC_hg38/Jurkat_ChRO-seq_1_TSSenrichment.png PEPPRO _OBJ_
### Calculate Pause Index (PI) (06-11 19:11:36) elapsed: 0.0 _TIME_
Missing stat 'Pause_index'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_tss.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_gene_body.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSS_density.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_gene_body_density.bed`
Found lock file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/lock.QC_hg38__Jurkat_ChRO-seq_1_pause_index.bed
Overwriting target...
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/QC_hg38/tmpztt2wubq` (45321,45322,45323)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.006GB.
PID: 45321; Command: join; Return code: 0; Memory used: 0.001GB
PID: 45323; Command: env; Return code: 0; Memory used: 0.006GB
PID: 45322; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/tmpztt2wubq | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}`
/bin/sh: -c: line 0: unexpected EOF while looking for matching `''
/bin/sh: -c: line 1: syntax error: unexpected end of file
### Pipeline failed at: (06-11 19:11:36) elapsed: 0.0 _TIME_
Total time: 0:00:01
Failure reason: Command 'awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/tmpztt2wubq | 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 Jurkat_ChRO-seq_1 --genome hg38 --input /project/shefflab/data//sra_fastq/SRR7616133.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol PRO --umi-len 6 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba27-28c0
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/
* Pipeline started at: (06-14 21:14:42) 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`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//sra_fastq/SRR7616133.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `12000`
* `new_start`: `False`
* `no_fifo`: `False`
* `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline`
* `paired_end`: `False`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `PRO`
* `recover`: `True`
* `sample_name`: `Jurkat_ChRO-seq_1`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `SINGLE`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `6`
* `verbosity`: `None`
----------------------------------------
Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//sra_fastq/SRR7616133.fastq.gz
> `File_mb` 1330.25 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-14 21:14:43) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz'
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/Jurkat_ChRO-seq_1_R1.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/Jurkat_ChRO-seq_1.fastq.gz']
### FASTQ processing: (06-14 21:14:43) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/fastq/processed_R1.flag`
### Plot adapter insertion distribution (06-14 21:14:43) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/cutadapt/Jurkat_ChRO-seq_1_R1_adapter_insertion_distribution.pdf`
> `Adapter insertion distribution` cutadapt/Jurkat_ChRO-seq_1_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/Jurkat_ChRO-seq_1_R1_adapter_insertion_distribution.png PEPPRO _OBJ_
### Prealignments (06-14 21:14:43) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-14 21:14:43) elapsed: 0.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap.fq
### Map to human_rDNA (06-14 21:14:43) elapsed: 0.0 _TIME_
### Map to genome (06-14 21:14:43) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam`
### Compress all unmapped read files (06-14 21:14:43) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/prealignments/Jurkat_ChRO-seq_1_human_rDNA_unmap.fq.gz`
### Calculate NRF, PBC1, and PBC2 (06-14 21:14:43) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam.bai`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_bamQC.tsv`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_unmap.bam`
### Split BAM by strand (06-14 21:14:43) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam`
### Calculate TSS enrichment (06-14 21:14:43) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSSenrichment.pdf`
> `TSS enrichment` QC_hg38/Jurkat_ChRO-seq_1_TSSenrichment.pdf TSS enrichment QC_hg38/Jurkat_ChRO-seq_1_TSSenrichment.png PEPPRO _OBJ_
### Calculate Pause Index (PI) (06-14 21:14:43) elapsed: 0.0 _TIME_
Missing stat 'Pause_index'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_tss.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_ensembl_gene_body.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSS_density.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_gene_body_density.bed`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/QC_hg38/tmp6gr4kvrx` (304870,304873,304875)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.004GB.
PID: 304870; Command: join; Return code: 0; Memory used: 0.001GB
PID: 304875; Command: env; Return code: 0; Memory used: 0.004GB
PID: 304873; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/tmp6gr4kvrx | 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/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.0149084) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/tmp6gr4kvrx > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_pause_index.bed` (304905)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.004GB.
PID: 304905; Command: awk; Return code: 0; Memory used: 0.002GB
> `sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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` 42.69 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_pause_index.bed` (304910)
Pause index plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.244GB.
PID: 304910; Command: Rscript; Return code: 0; Memory used: 0.244GB
> `Pause index` QC_hg38/Jurkat_ChRO-seq_1_pause_index.pdf Pause index QC_hg38/Jurkat_ChRO-seq_1_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_pause_index.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_pause_index.bed` (304933)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.244GB.
PID: 304933; Command: pigz; Return code: 0; Memory used: 0.004GB
### Calculate Fraction of Reads in pre-mature mRNA (06-14 21:14:49) elapsed: 7.0 _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/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam`
21338079 7688297
> `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/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam`
21338079 7358614
> `Minus_FRiP` 0.34 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/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/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_gene_sort.bed` (305367,305368)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.244GB.
PID: 305367; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 305368; Command: bedtools; Return code: 0; Memory used: 0.006GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_gene_coverage.bed` (305370)
Command completed. Elapsed time: 0:00:29. Running peak memory: 0.244GB.
PID: 305370; Command: bedtools; Return code: 0; Memory used: 0.085GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/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/Jurkat_ChRO-seq_1/raw/hg38_annotations.bed.gz` (305399)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.244GB.
PID: 305399; Command: ln; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/hg38_annotations.bed` (305400)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.244GB.
PID: 305400; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-14 21:15:57) elapsed: 68.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/raw/hg38_annotations.bed` (305409)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.244GB.
PID: 305409; Command: awk; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Enhancer_sort.bed` (305412,305413,305414,305415)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.244GB.
PID: 305412; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 305413; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 305415; Command: bedtools; Return code: 0; Memory used: 0.046GB
PID: 305414; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Enhancer_plus_coverage.bed` (305417)
Command completed. Elapsed time: 0:00:11. Running peak memory: 0.244GB.
PID: 305417; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Enhancer_minus_coverage.bed` (305428)
Command completed. Elapsed time: 0:00:11. Running peak memory: 0.244GB.
PID: 305428; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_sort.bed` (305538,305539,305540,305541)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.244GB.
PID: 305538; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 305539; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 305541; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 305540; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_plus_coverage.bed` (305554)
Command completed. Elapsed time: 0:00:12. Running peak memory: 0.244GB.
PID: 305554; Command: bedtools; Return code: 0; Memory used: 0.037GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_minus_coverage.bed` (305661)
Command completed. Elapsed time: 0:00:12. Running peak memory: 0.244GB.
PID: 305661; Command: bedtools; Return code: 0; Memory used: 0.031GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_Flanking_Region"` (305675)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.244GB.
PID: 305675; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_Flanking_Region_sort.bed` (305676,305677,305678,305679)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.244GB.
PID: 305676; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 305678; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 305677; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 305679; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_Flanking_Region_plus_coverage.bed` (305682)
Command completed. Elapsed time: 0:00:13. Running peak memory: 0.244GB.
PID: 305682; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_Flanking_Region_minus_coverage.bed` (307252)
Command completed. Elapsed time: 0:00:12. Running peak memory: 0.244GB.
PID: 307252; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/5_UTR"` (316865)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.244GB.
PID: 316865; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/5_UTR_sort.bed` (317008,317009,317010,317011)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.244GB.
PID: 317008; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 317009; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 317011; Command: bedtools; Return code: 0; Memory used: 0.012GB
PID: 317010; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_5_UTR_plus_coverage.bed` (317625)
Command completed. Elapsed time: 0:00:13. Running peak memory: 0.244GB.
PID: 317625; Command: bedtools; Return code: 0; Memory used: 0.028GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_5_UTR_minus_coverage.bed` (332877)
Command completed. Elapsed time: 0:00:12. Running peak memory: 0.244GB.
PID: 332877; Command: bedtools; Return code: 0; Memory used: 0.02GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/3_UTR"` (348684)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.244GB.
PID: 348684; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/3_UTR_sort.bed` (348882,348918,348937,348945)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.244GB.
PID: 348882; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 348918; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 348945; Command: bedtools; Return code: 0; Memory used: 0.013GB
PID: 348937; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_3_UTR_plus_coverage.bed` (350591)
Command completed. Elapsed time: 0:00:13. Running peak memory: 0.244GB.
PID: 350591; Command: bedtools; Return code: 0; Memory used: 0.013GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_3_UTR_minus_coverage.bed` (374792)
Command completed. Elapsed time: 0:00:14. Running peak memory: 0.244GB.
PID: 374792; Command: bedtools; Return code: 0; Memory used: 0.014GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Exon_sort.bed` (397491,397549,397556,397558)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.244GB.
PID: 397491; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 397549; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 397558; Command: bedtools; Return code: 0; Memory used: 0.177GB
PID: 397556; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Exon_plus_coverage.bed` (403618)
Command completed. Elapsed time: 0:00:15. Running peak memory: 0.244GB.
PID: 403618; Command: bedtools; Return code: 0; Memory used: 0.057GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Exon_minus_coverage.bed` (429156)
Command completed. Elapsed time: 0:00:14. Running peak memory: 0.244GB.
PID: 429156; Command: bedtools; Return code: 0; Memory used: 0.035GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Intron_sort.bed` (447116,447165,447182,447189)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.244GB.
PID: 447116; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 447182; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 447165; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 447189; Command: bedtools; Return code: 0; Memory used: 0.083GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Intron_plus_coverage.bed` (449088)
Command completed. Elapsed time: 0:00:15. Running peak memory: 0.244GB.
PID: 449088; Command: bedtools; Return code: 0; Memory used: 0.045GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Intron_minus_coverage.bed` (1087)
Command completed. Elapsed time: 0:00:14. Running peak memory: 0.244GB.
PID: 1087; Command: bedtools; Return code: 0; Memory used: 0.049GB
### Plot cFRiF/FRiF (06-14 21:19:07) elapsed: 190.0 _TIME_
> `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s Jurkat_ChRO-seq_1 -z 3099922541 -n 10780321 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Intron_plus_coverage.bed` (1141)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:36. Running peak memory: 0.469GB.
PID: 1141; Command: Rscript; Return code: 0; Memory used: 0.469GB
> `cFRiF` QC_hg38/Jurkat_ChRO-seq_1_cFRiF.pdf cFRiF QC_hg38/Jurkat_ChRO-seq_1_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s Jurkat_ChRO-seq_1 -z 3099922541 -n 10780321 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_Intron_plus_coverage.bed` (1220)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:26. Running peak memory: 0.469GB.
PID: 1220; Command: Rscript; Return code: 0; Memory used: 0.467GB
> `FRiF` QC_hg38/Jurkat_ChRO-seq_1_FRiF.pdf FRiF QC_hg38/Jurkat_ChRO-seq_1_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-14 21:20:10) elapsed: 63.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/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/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_exons_sort.bed` (1653,1654)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.469GB.
PID: 1654; Command: bedtools; Return code: 0; Memory used: 0.099GB
PID: 1653; Command: grep; Return code: 0; Memory used: 0.004GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/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/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_introns_sort.bed` (1668,1669,1670)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.469GB.
PID: 1668; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 1670; Command: bedtools; Return code: 0; Memory used: 0.006GB
PID: 1669; Command: bedtools; Return code: 0; Memory used: 0.036GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_exons_coverage.bed` (1694)
Command completed. Elapsed time: 0:00:22. Running peak memory: 0.469GB.
PID: 1694; Command: bedtools; Return code: 0; Memory used: 0.039GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_introns_coverage.bed` (1756)
Command completed. Elapsed time: 0:00:25. Running peak memory: 0.469GB.
PID: 1756; Command: bedtools; Return code: 0; Memory used: 0.068GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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]/21.338079)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_exons_rpkm.bed` (1778,1779,1780)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.469GB.
PID: 1778; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 1780; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 1779; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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]/21.338079)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_introns_rpkm.bed` (1782,1783,1784)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.469GB.
PID: 1782; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 1784; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 1783; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_exon_intron_ratios.bed` (1786,1787,1788)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.469GB.
PID: 1786; Command: join; Return code: 0; Memory used: 0.001GB
PID: 1788; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 1787; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_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` 1.19 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_mRNA_contamination.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_exon_intron_ratios.bed --annotate` (1795)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.469GB.
PID: 1795; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `mRNA contamination` QC_hg38/Jurkat_ChRO-seq_1_mRNA_contamination.pdf mRNA contamination QC_hg38/Jurkat_ChRO-seq_1_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_exon_intron_ratios.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/QC_hg38/Jurkat_ChRO-seq_1_exon_intron_ratios.bed` (1815)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.469GB.
PID: 1815; Command: pigz; Return code: 0; Memory used: 0.003GB
### Produce bigWig files (06-14 21:21:13) elapsed: 63.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam` (1823)
Command completed. Elapsed time: 0:00:07. Running peak memory: 0.469GB.
PID: 1823; Command: samtools; Return code: 0; Memory used: 0.01GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 21338079.0` (1830)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_plus.bam'
Temporary files will be stored in: 'tmp_Jurkat_ChRO-seq_1_plus_cuttrace_gbzfszua'
Processing with 4 cores...
stdin is empty of data
stdin is empty of data
stdin is empty of data
Discarding 122 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr9_KI270717v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr15_KI270727v1_random', 'chr22_KI270732v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', '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_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_KI270743v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270742v1']
Keeping 73 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_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270538v1', 'chrUn_KI270583v1', 'chrUn_KI270579v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_GL000213v1', 'chrUn_KI270744v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 73 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_plus_exact_body_0-mer.bw'
Merging 73 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:06:37. Running peak memory: 2.442GB.
PID: 1830; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.442GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam` (311235)
Command completed. Elapsed time: 0:00:07. Running peak memory: 2.442GB.
PID: 311235; Command: samtools; Return code: 0; Memory used: 0.009GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 21338079.0` (311251)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/aligned_hg38/Jurkat_ChRO-seq_1_minus.bam'
Temporary files will be stored in: 'tmp_Jurkat_ChRO-seq_1_minus_cuttrace_or0c10qu'
Processing with 4 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
stdin is empty of data
Discarding 126 chunk(s) of reads: ['chrM', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr14_KI270725v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', '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_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1']
Keeping 69 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_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_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_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chrUn_KI270442v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270538v1', 'chrUn_KI270580v1', 'chrUn_KI270330v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 69 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_minus_exact_body_0-mer.bw'
Merging 69 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/Jurkat_ChRO-seq_1/signal_hg38/Jurkat_ChRO-seq_1_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:06:27. Running peak memory: 3.351GB.
PID: 311251; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.351GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:19:54
* Total elapsed time (all runs): 1:16:55
* Peak memory (this run): 3.3511 GB
* Pipeline completed time: 2020-06-14 21:34:30