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.fastqCommand 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 removedCommand 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