Pipeline run code and environment:
- Command:
/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_PRO-seq_100 --genome hg38 --input /project/shefflab/data//sra_fastq/SRR1554311.fastq.gz /project/shefflab/data//sra_fastq/SRR1554312.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 32 -M 32000 --protocol PRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R
- Compute host: udc-aj40-15c0
- Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
- Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/
- Pipeline started at: (06-11 19:07:43) elapsed: 3.0 TIME
Version log:
- Python version: 3.6.6
- Pypiper dir:
/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper
- Pypiper version: 0.12.1
- Pipeline dir:
/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines
- Pipeline version: 0.9.8
- Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
- Pipeline branch: * master
- Pipeline date: 2020-06-09 11:36:49 -0400
- Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
Arguments passed to pipeline:
TSS_name
:None
adapter
:cutadapt
anno_name
:None
complexity
:False
config_file
:peppro.yaml
cores
:32
coverage
:False
dedup
:seqkit
dirty
:True
ensembl_gene_body
:None
ensembl_tss
:None
exon_name
:None
force_follow
:False
genome_assembly
:hg38
input
:['/project/shefflab/data//sra_fastq/SRR1554311.fastq.gz', '/project/shefflab/data//sra_fastq/SRR1554312.fastq.gz']
input2
:None
intron_name
:None
keep
:False
logdev
:False
max_len
:-1
mem
:32000
new_start
:False
no_fifo
:False
output_parent
:/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline
paired_end
:False
pre_name
:None
prealignments
:['human_rDNA']
prioritize
:False
protocol
:PRO
recover
:True
sample_name
:K562_PRO-seq_100
scale
:True
search_file
:None
silent
:False
single_or_paired
:SINGLE
sob
:False
testmode
:False
trimmer
:seqtk
umi_len
:0
verbosity
:None
Local input file: /project/shefflab/data//sra_fastq/SRR1554311.fastq.gz
File_mb
38578.5 PEPPRO RES
Read_type
SINGLE PEPPRO RES
Genome
hg38 PEPPRO RES Detected PRO input
Merge/link and fastq conversion: (06-11 19:07:44) elapsed: 1.0 TIME
Number of input file sets: 1
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/K562_PRO-seq_100.merged.fastq.gz
cat /project/shefflab/data//sra_fastq/SRR1554311.fastq.gz /project/shefflab/data//sra_fastq/SRR1554312.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/K562_PRO-seq_100.merged.fastq.gz
(239583)Command completed. Elapsed time: 0:02:48. Running peak memory: 0.003GB.
PID: 239583; Command: cat; Return code: 0; Memory used: 0.003GB
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/K562_PRO-seq_100.merged.fastq.gz'
Found .fastq.gz file
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1.fastq
pigz -f -p 32 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/K562_PRO-seq_100.merged.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1.fastq
(240015)Command completed. Elapsed time: 0:14:07. Running peak memory: 0.003GB.
PID: 240015; Command: pigz; Return code: 0; Memory used: 0.003GB
Raw_reads
496581677 PEPPRO RES
Fastq_reads
496581677 PEPPRO RES ['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/K562_PRO-seq_100.merged.fastq.gz']
FASTQ processing: (06-11 19:36:58) elapsed: 1755.0 TIME
cutadapt --version
Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1_processed.fastq
(cutadapt -j 32 -m 2 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt
(243484)Command completed. Elapsed time: 0:14:01. Running peak memory: 11.493GB.
PID: 243484; Command: cutadapt; Return code: 0; Memory used: 11.493GB
seqtk trimfq -b 0 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1_noadap.fastq | seqtk seq -L 2 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1_processed.fastq
(245187,245188)Command completed. Elapsed time: 0:09:01. Running peak memory: 11.493GB.
PID: 245187; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 245188; Command: seqtk; Return code: 0; Memory used: 0.002GB
grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt | awk '{print $(NF-1)}'
Reads_with_adapter
423059183.0 PEPPRO RES
grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt | awk '{print $(NF-1)}'
awk '{sum+=$1*$2} END {printf "%.0f", sum}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt
wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1_short.fastq | awk '{print $1}'
Uninformative_adapter_reads
12437983.0 PEPPRO RES
Pct_uninformative_adapter_reads
2.5047 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastqc/K562_PRO-seq_100_R1_processed_fastqc.html
echo '### Calculate the number of trimmed reads'
(247019)
Calculate the number of trimmed reads
Command completed. Elapsed time: 0:00:00. Running peak memory: 11.493GB.
PID: 247019; Command: echo; Return code: 0; Memory used: 0.0GB
Evaluating read trimming
Trimmed_reads
484143694 PEPPRO RES
Trim_loss_rate
2.5 PEPPRO RES Targetless command, running...
fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1_processed.fastq
(247474)Started analysis of K562_PRO-seq_100_R1_processed.fastq Approx 5% complete for K562_PRO-seq_100_R1_processed.fastq Approx 10% complete for K562_PRO-seq_100_R1_processed.fastq Approx 15% complete for K562_PRO-seq_100_R1_processed.fastq Approx 20% complete for K562_PRO-seq_100_R1_processed.fastq Approx 25% complete for K562_PRO-seq_100_R1_processed.fastq Approx 30% complete for K562_PRO-seq_100_R1_processed.fastq Approx 35% complete for K562_PRO-seq_100_R1_processed.fastq Approx 40% complete for K562_PRO-seq_100_R1_processed.fastq Approx 45% complete for K562_PRO-seq_100_R1_processed.fastq Approx 50% complete for K562_PRO-seq_100_R1_processed.fastq Approx 55% complete for K562_PRO-seq_100_R1_processed.fastq Approx 60% complete for K562_PRO-seq_100_R1_processed.fastq Approx 65% complete for K562_PRO-seq_100_R1_processed.fastq Approx 70% complete for K562_PRO-seq_100_R1_processed.fastq Approx 75% complete for K562_PRO-seq_100_R1_processed.fastq Approx 80% complete for K562_PRO-seq_100_R1_processed.fastq Approx 85% complete for K562_PRO-seq_100_R1_processed.fastq Approx 90% complete for K562_PRO-seq_100_R1_processed.fastq Approx 95% complete for K562_PRO-seq_100_R1_processed.fastq Analysis complete for K562_PRO-seq_100_R1_processed.fastqCommand completed. Elapsed time: 0:26:15. Running peak memory: 11.493GB.
PID: 247474; Command: fastqc; Return code: 0; Memory used: 0.3GB
FastQC report r1
fastqc/K562_PRO-seq_100_R1_processed_fastqc.html FastQC report r1 None PEPPRO OBJ Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/processed_R1.flag
touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/processed_R1.flag
(250743)Command completed. Elapsed time: 0:00:00. Running peak memory: 11.493GB.
PID: 250743; Command: touch; Return code: 0; Memory used: 0.002GB
Plot adapter insertion distribution (06-11 20:34:31) elapsed: 3452.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_adapter_insertion_distribution.pdf
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R cutadapt -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt
(250749)Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 11.493GB.
PID: 250749; Command: Rscript; Return code: 0; Memory used: 0.204GB
Adapter insertion distribution
cutadapt/K562_PRO-seq_100_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_PRO-seq_100_R1_adapter_insertion_distribution.png PEPPRO OBJ Missing stat 'Peak_adapter_insertion_size'
awk '/count/,0' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt | awk 'NR>2 {print prev} {prev=$0}' | awk '{if ($3/$2 < 0.01) print $1, $2}' | awk 'BEGIN{max= 0; max_len=0; len=0}{if ($2>0+max) {max=$2; len=$1}; max_len=$1} END{print max_len-len}'
Peak_adapter_insertion_size
34 PEPPRO RES Missing stat 'Degradation_ratio'
Calculating degradation ratio (06-11 20:34:37) elapsed: 6.0 TIME
awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt | awk '{ if ($1 == 10) {status = 1}} END {if (status) {print status} else {print 0}}'
awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt | awk '{ if ($1 == 20) {status = 1}} END {if (status) {print status} else {print 0}}'
awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt | awk '{ if ($1 == 30) {status = 1}} END {if (status) {print status} else {print 0}}'
awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt | awk '{ if ($1 == 40) {status = 1}} END {if (status) {print status} else {print 0}}'
awk '/count/,0' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_cutadapt.txt | awk 'NR>2 {print prev} {prev=$0}' | awk '{if ($3/$2 < 0.01) print $1, $2}' | awk '{a[NR]=$1; b[NR]=$2; max_len=$1}{if ($1 > max_len) {max_len=$1}} END{ for (i in a) print 1+max_len-a[i], b[i]}' | sort -nk1 | awk '($1 <= 20 && $1 >= 10){degradedSum += $2}; ($1 >= 30 && $1 <= 40){intactSum += $2} END {if (intactSum < 1) {intactSum = 1} print degradedSum/intactSum}'
Degradation_ratio
0.2312 PEPPRO RES
Prealignments (06-11 20:34:37) elapsed: 0.0 TIME
Prealignment assemblies: ['human_rDNA']
Map to human_rDNA (06-11 20:34:37) elapsed: 0.0 TIME
(bowtie2 -p 32 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id K562_PRO-seq_100 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/prealignments/K562_PRO-seq_100_human_rDNA_unmap.fq 2>&1 > /dev/null)
Missing stat 'Aligned_reads_human_rDNA' 484143694 reads; of these: 484143694 (100.00%) were unpaired; of these: 439463330 (90.77%) aligned 0 times 44680364 (9.23%) aligned exactly 1 time 0 (0.00%) aligned >1 times 9.23% overall alignment rate
Aligned_reads_human_rDNA
44680364.0 PEPPRO RES
Alignment_rate_human_rDNA
9.23 PEPPRO RES
Map to genome (06-11 21:34:48) elapsed: 3611.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam
bowtie2 -p 32 --very-sensitive --rg-id K562_PRO-seq_100 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/prealignments/K562_PRO-seq_100_human_rDNA_unmap.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/tmplun3n5k_ -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_temp.bam
(258021,258027,258028)439463330 reads; of these: 439463330 (100.00%) were unpaired; of these: 5393540 (1.23%) aligned 0 times 328159166 (74.67%) aligned exactly 1 time 105910624 (24.10%) aligned >1 times 98.77% overall alignment rate [bam_sort_core] merging from 142 files and 1 in-memory blocks...Command completed. Elapsed time: 3:21:41. Running peak memory: 11.493GB.
PID: 258021; Command: bowtie2; Return code: 0; Memory used: 4.227GB
PID: 258027; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 258028; Command: samtools; Return code: 0; Memory used: 0.906GB
samtools view -q 10 -b -@ 32 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam
(279311)Command completed. Elapsed time: 0:08:44. Running peak memory: 11.493GB.
PID: 279311; Command: samtools; Return code: 0; Memory used: 0.036GB
samtools depth -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'
Mapped_reads
434069790 PEPPRO RES
QC_filtered_reads
46741044 PEPPRO RES
Aligned_reads
387328746 PEPPRO RES
Alignment_rate
80.0 PEPPRO RES
Total_efficiency
78.0 PEPPRO RES
Read_depth
29.61 PEPPRO RES
Compress all unmapped read files (06-12 02:01:41) elapsed: 16013.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/prealignments/K562_PRO-seq_100_human_rDNA_unmap.fq.gz
pigz -f -p 32 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/prealignments/K562_PRO-seq_100_human_rDNA_unmap.fq
(286219)Command completed. Elapsed time: 0:06:42. Running peak memory: 11.493GB.
PID: 286219; Command: pigz; Return code: 0; Memory used: 0.024GB
Missing stat 'Mitochondrial_reads'
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_temp.bam.bai
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_temp.bam
(286889)Command completed. Elapsed time: 0:06:33. Running peak memory: 11.493GB.
PID: 286889; Command: samtools; Return code: 0; Memory used: 0.027GB
samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3
Mitochondrial_reads
9149071 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_noMT.bam
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam
(287540)Command completed. Elapsed time: 0:05:38. Running peak memory: 11.493GB.
PID: 287540; Command: samtools; Return code: 0; Memory used: 0.024GB
samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam | cut -f 1-2 | awk '{print $1, 0, $2}' | grep -vwe 'chrM' -vwe 'chrMT' -vwe 'M' -vwe 'MT' -vwe 'rCRSd' -vwe 'rCRSd_3k' > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/chr_sizes.bed
(288310,288311,288312,288313)Command completed. Elapsed time: 0:00:00. Running peak memory: 11.493GB.
PID: 288312; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 288310; Command: samtools; Return code: 0; Memory used: 0.01GB
PID: 288313; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 288311; Command: cut; Return code: 0; Memory used: 0.001GB
samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/chr_sizes.bed -b -@ 32 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_noMT.bam
(288315)Command completed. Elapsed time: 0:04:16. Running peak memory: 11.493GB.
PID: 288315; Command: samtools; Return code: 0; Memory used: 0.037GB
mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam
(288608)Command completed. Elapsed time: 0:00:03. Running peak memory: 11.493GB.
PID: 288608; Command: mv; Return code: 0; Memory used: 0.002GB
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam
(288612)Command completed. Elapsed time: 0:05:31. Running peak memory: 11.493GB.
PID: 288612; Command: samtools; Return code: 0; Memory used: 0.024GB
Missing stat 'Maximum_read_length'
samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-
Maximum_read_length
100 PEPPRO RES Missing stat 'Genome_size'
awk '{sum+=$2} END {printf "%.0f", sum}' /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes
Genome_size
3099922541 PEPPRO RES
Calculate NRF, PBC1, and PBC2 (06-12 02:47:15) elapsed: 2733.0 TIME
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam.bai
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_bamQC.tsv
/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam -c 32 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_bamQC.tsv
(291051)Configured logger 'root' using pararead v0.6 Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam' Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/tmp_K562_PRO-seq_100_sort_440xxpb4' Processing with 32 cores... Discarding 81 chunk(s) of reads: ['chrM', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270593v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1'] Keeping 114 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270310v1', 'chrUn_KI270411v1', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270515v1', 'chrUn_KI270538v1', 'chrUn_KI270583v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']Command completed. Elapsed time: 0:04:01. Running peak memory: 16.596GB.
PID: 291051; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 16.596GB
awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_bamQC.tsv
awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_bamQC.tsv
awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_bamQC.tsv
NRF
0.28 PEPPRO RES
PBC1
0.54 PEPPRO RES
PBC2
3.89 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_unmap.bam
samtools view -b -@ 32 -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_unmap.bam
(291601)Command completed. Elapsed time: 0:01:11. Running peak memory: 16.596GB.
PID: 291601; Command: samtools; Return code: 0; Memory used: 0.017GB
samtools view -c -f 4 -@ 32 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_temp.bam
Unmapped_reads
5393540 PEPPRO RES
Split BAM by strand (06-12 02:53:38) elapsed: 383.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam
samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam
(291818)Command completed. Elapsed time: 0:27:15. Running peak memory: 16.596GB.
PID: 291818; Command: samtools; Return code: 0; Memory used: 0.006GB
samtools view -bh -f 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam
(294786)Command completed. Elapsed time: 0:25:39. Running peak memory: 16.596GB.
PID: 294786; Command: samtools; Return code: 0; Memory used: 0.006GB
Calculate TSS enrichment (06-12 03:46:32) elapsed: 3174.0 TIME
Missing stat 'TSS_non-coding_score'
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/plus_TSS.tsv
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/minus_TSS.tsv
sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed
(297442)Command completed. Elapsed time: 0:00:00. Running peak memory: 16.596GB.
PID: 297442; Command: sed; Return code: 0; Memory used: 0.002GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_plus_TssEnrichment.txt
/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/plus_TSS.tsv -p ends -c 32 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_plus_TssEnrichment.txt
(297448)Command completed. Elapsed time: 0:00:36. Running peak memory: 16.596GB.
PID: 297448; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 1.744GB
TSS_coding_score
13.9 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_minus_TssEnrichment.txt
/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/minus_TSS.tsv -p ends -c 32 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_minus_TssEnrichment.txt
(297553)Command completed. Elapsed time: 0:00:27. Running peak memory: 16.596GB.
PID: 297553; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 2.008GB
TSS_non-coding_score
5.8 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_TSSenrichment.pdf
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_minus_TssEnrichment.txt
(297652)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_minus_TssEnrichment.txt
geom_smooth()
using formula 'y ~ x'
geom_smooth()
using formula 'y ~ x'
geom_smooth()
using formula 'y ~ x'
geom_smooth()
using formula 'y ~ x'
TSS enrichment plot completed!
Command completed. Elapsed time: 0:00:07. Running peak memory: 16.596GB.
PID: 297652; Command: Rscript; Return code: 0; Memory used: 0.204GB
TSS enrichment
QC_hg38/K562_PRO-seq_100_TSSenrichment.pdf TSS enrichment QC_hg38/K562_PRO-seq_100_TSSenrichment.png PEPPRO OBJ Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt
samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam | grep 'SN:' | awk -F':' '{print $2,$3}' | awk -F' ' -v OFS=' ' '{print $1,$3}' > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt
(297684,297685,297686,297687)Command completed. Elapsed time: 0:00:00. Running peak memory: 16.596GB.
PID: 297684; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 297686; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 297685; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 297687; Command: awk; Return code: 0; Memory used: 0.0GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_keep.txt
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_keep.txt
(297689)Command completed. Elapsed time: 0:00:00. Running peak memory: 16.596GB.
PID: 297689; Command: cut; Return code: 0; Memory used: 0.002GB
Calculate Pause Index (PI) (06-12 03:47:43) elapsed: 71.0 TIME
Missing stat 'Pause_index'
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_ensembl_tss.bed
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_ensembl_gene_body.bed
grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_TSS.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_ensembl_tss.bed
(297691,297692)Command completed. Elapsed time: 0:00:02. Running peak memory: 16.596GB.
PID: 297691; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 297692; Command: bedtools; Return code: 0; Memory used: 0.093GB
grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_gene_body.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_ensembl_gene_body.bed
(297696,297697)Command completed. Elapsed time: 0:00:00. Running peak memory: 16.596GB.
PID: 297696; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 297697; Command: bedtools; Return code: 0; Memory used: 0.005GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_TSS_density.bed
bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4,4 -k7,7nr | sort -k4,4 -u > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_TSS_density.bed
(297699,297700,297701,297702)Command completed. Elapsed time: 0:08:08. Running peak memory: 16.596GB.
PID: 297699; Command: bedtools; Return code: 0; Memory used: 0.103GB
PID: 297701; Command: sort; Return code: 0; Memory used: 0.01GB
PID: 297700; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 297702; Command: sort; Return code: 0; Memory used: 0.012GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_gene_body_density.bed
bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_gene_body_density.bed
(298620,298626,298627)Command completed. Elapsed time: 0:14:05. Running peak memory: 16.596GB.
PID: 298626; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 298620; Command: bedtools; Return code: 0; Memory used: 1.022GB
PID: 298627; Command: sort; Return code: 0; Memory used: 0.005GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_pause_index.bed
join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_gene_body_density.bed | awk -v OFS=' ' '{ if ($5 == "+"){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2), ($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}' | env LC_COLLATE=C sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/tmpuv374kz8
(299969,299975,299976)Command completed. Elapsed time: 0:00:01. Running peak memory: 16.596GB.
PID: 299969; Command: join; Return code: 0; Memory used: 0.001GB
PID: 299976; Command: env; Return code: 0; Memory used: 0.006GB
PID: 299975; Command: awk; Return code: 0; Memory used: 0.001GB
awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/tmpuv374kz8 | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}
/bin/sh: -c: line 0: unexpected EOF while looking for matching `'' /bin/sh: -c: line 1: syntax error: unexpected end of file
Pipeline failed at: (06-12 04:09:58) elapsed: 1335.0 TIME
Total time: 9:02:18 Failure reason: Command 'awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/tmpuv374kz8 | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}' returned non-zero exit status 1.
Pipeline run code and environment:
- Command:
/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_PRO-seq_100 --genome hg38 --input /project/shefflab/data//sra_fastq/SRR1554311.fastq.gz /project/shefflab/data//sra_fastq/SRR1554312.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 32 -M 32000 --protocol PRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R
- Compute host: udc-aj37-17c0
- Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
- Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/
- Pipeline started at: (06-14 21:10:54) elapsed: 6.0 TIME
Version log:
- Python version: 3.6.6
- Pypiper dir:
/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper
- Pypiper version: 0.12.1
- Pipeline dir:
/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines
- Pipeline version: 0.9.8
- Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
- Pipeline branch: * master
- Pipeline date: 2020-06-09 11:36:49 -0400
- Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
Arguments passed to pipeline:
TSS_name
:None
adapter
:cutadapt
anno_name
:None
complexity
:False
config_file
:peppro.yaml
cores
:32
coverage
:False
dedup
:seqkit
dirty
:True
ensembl_gene_body
:None
ensembl_tss
:None
exon_name
:None
force_follow
:False
genome_assembly
:hg38
input
:['/project/shefflab/data//sra_fastq/SRR1554311.fastq.gz', '/project/shefflab/data//sra_fastq/SRR1554312.fastq.gz']
input2
:None
intron_name
:None
keep
:False
logdev
:False
max_len
:-1
mem
:32000
new_start
:False
no_fifo
:False
output_parent
:/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline
paired_end
:False
pre_name
:None
prealignments
:['human_rDNA']
prioritize
:False
protocol
:PRO
recover
:True
sample_name
:K562_PRO-seq_100
scale
:True
search_file
:None
silent
:False
single_or_paired
:SINGLE
sob
:False
testmode
:False
trimmer
:seqtk
umi_len
:0
verbosity
:None
Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/PEPPRO_failed.flag' Local input file: /project/shefflab/data//sra_fastq/SRR1554311.fastq.gz
File_mb
38578.5 PEPPRO RES
Read_type
SINGLE PEPPRO RES
Genome
hg38 PEPPRO RES Detected PRO input
Merge/link and fastq conversion: (06-14 21:10:55) elapsed: 1.0 TIME
Number of input file sets: 1
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/K562_PRO-seq_100.merged.fastq.gz
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/K562_PRO-seq_100.merged.fastq.gz'
Found .fastq.gz file
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/K562_PRO-seq_100_R1.fastq
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/K562_PRO-seq_100.merged.fastq.gz']
FASTQ processing: (06-14 21:10:55) elapsed: 0.0 TIME
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/fastq/processed_R1.flag
Plot adapter insertion distribution (06-14 21:10:55) elapsed: 0.0 TIME
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/cutadapt/K562_PRO-seq_100_R1_adapter_insertion_distribution.pdf
Adapter insertion distribution
cutadapt/K562_PRO-seq_100_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_PRO-seq_100_R1_adapter_insertion_distribution.png PEPPRO OBJ
Prealignments (06-14 21:10:55) elapsed: 0.0 TIME
Prealignment assemblies: ['human_rDNA']
Map to human_rDNA (06-14 21:10:55) elapsed: 0.0 TIME
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/prealignments/K562_PRO-seq_100_human_rDNA_unmap.fq
Map to genome (06-14 21:10:55) elapsed: 0.0 TIME
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam
Compress all unmapped read files (06-14 21:10:55) elapsed: 0.0 TIME
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/prealignments/K562_PRO-seq_100_human_rDNA_unmap.fq.gz
Calculate NRF, PBC1, and PBC2 (06-14 21:10:55) elapsed: 0.0 TIME
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam.bai
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_bamQC.tsv
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_unmap.bam
Split BAM by strand (06-14 21:10:55) elapsed: 0.0 TIME
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam
Calculate TSS enrichment (06-14 21:10:55) elapsed: 0.0 TIME
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_TSSenrichment.pdf
TSS enrichment
QC_hg38/K562_PRO-seq_100_TSSenrichment.pdf TSS enrichment QC_hg38/K562_PRO-seq_100_TSSenrichment.png PEPPRO OBJ
Calculate Pause Index (PI) (06-14 21:10:55) elapsed: 0.0 TIME
Missing stat 'Pause_index'
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_ensembl_tss.bed
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_ensembl_gene_body.bed
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_TSS_density.bed
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_gene_body_density.bed
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_pause_index.bed
join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_gene_body_density.bed | awk -v OFS=' ' '{ if ($5 == "+"){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2), ($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}' | env LC_COLLATE=C sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/tmpot1hg31_
(280310,280311,280312)Command completed. Elapsed time: 0:00:00. Running peak memory: 0.006GB.
PID: 280310; Command: join; Return code: 0; Memory used: 0.001GB
PID: 280312; Command: env; Return code: 0; Memory used: 0.006GB
PID: 280311; Command: awk; Return code: 0; Memory used: 0.001GB
awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/tmpot1hg31_ | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}'
Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_pause_index.bed
awk -v OFS=' ' '{ if ($5 > 0.208447) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/tmpot1hg31_ > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_pause_index.bed
(280320)Command completed. Elapsed time: 0:00:00. Running peak memory: 0.006GB.
PID: 280320; Command: awk; Return code: 0; Memory used: 0.004GB
sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_pause_index.bed | awk ' { a[i++]=$5; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'
Pause_index
10.96 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_pause_index.pdf
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R pi --annotate -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_pause_index.bed
(280325)Pause index plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.212GB.
PID: 280325; Command: Rscript; Return code: 0; Memory used: 0.212GB
Pause index
QC_hg38/K562_PRO-seq_100_pause_index.pdf Pause index QC_hg38/K562_PRO-seq_100_pause_index.png PEPPRO OBJ Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_pause_index.bed.gz
pigz -f -p 32 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_pause_index.bed
(280358)Command completed. Elapsed time: 0:00:00. Running peak memory: 0.212GB.
PID: 280358; Command: pigz; Return code: 0; Memory used: 0.002GB
Calculate Fraction of Reads in pre-mature mRNA (06-14 21:11:01) elapsed: 6.0 TIME
Missing stat 'Plus_FRiP'
samtools view -@ 4 -c -L /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam
387328746 138157932
Plus_FRiP
0.36 PEPPRO RES Missing stat 'Minus_FRiP'
samtools view -@ 4 -c -L /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam
387328746 131399421
Minus_FRiP
0.34 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_gene_coverage.bed
grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_gene_sort.bed
(331289,331339)Command completed. Elapsed time: 0:00:01. Running peak memory: 0.212GB.
PID: 331289; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 331339; Command: bedtools; Return code: 0; Memory used: 0.004GB
bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_gene_coverage.bed
(331715)Command completed. Elapsed time: 0:15:16. Running peak memory: 1.021GB.
PID: 331715; Command: bedtools; Return code: 0; Memory used: 1.021GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/hg38_annotations.bed
ln -sf /project/shefflab/genomes/hg38/feat_annotation/default/hg38_annotations.bed.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/hg38_annotations.bed.gz
(393358)Command completed. Elapsed time: 0:00:00. Running peak memory: 1.021GB.
PID: 393358; Command: ln; Return code: 0; Memory used: 0.002GB
pigz -f -p 32 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/hg38_annotations.bed
(393364)Command completed. Elapsed time: 0:00:00. Running peak memory: 1.021GB.
PID: 393364; Command: pigz; Return code: 0; Memory used: 0.002GB
Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-14 21:37:32) elapsed: 1590.0 TIME
cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/hg38_annotations.bed | sort -u
Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Enhancer
awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/raw/hg38_annotations.bed
(393373)Command completed. Elapsed time: 0:00:01. Running peak memory: 1.021GB.
PID: 393373; Command: awk; Return code: 0; Memory used: 0.002GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Enhancer_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Enhancer_sort.bed
(393375,393376,393377,393378)Command completed. Elapsed time: 0:00:01. Running peak memory: 1.021GB.
PID: 393375; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 393376; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 393378; Command: bedtools; Return code: 0; Memory used: 0.048GB
PID: 393377; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Enhancer_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Enhancer_plus_coverage.bed
(393381)Command completed. Elapsed time: 0:04:20. Running peak memory: 1.021GB.
PID: 393381; Command: bedtools; Return code: 0; Memory used: 0.037GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Enhancer_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Enhancer_minus_coverage.bed
(393904)Command completed. Elapsed time: 0:04:08. Running peak memory: 1.021GB.
PID: 393904; Command: bedtools; Return code: 0; Memory used: 0.068GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_sort.bed
(394351,394352,394353,394354)Command completed. Elapsed time: 0:00:00. Running peak memory: 1.021GB.
PID: 394351; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 394352; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 394354; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 394353; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_plus_coverage.bed
(394356)Command completed. Elapsed time: 0:05:01. Running peak memory: 1.021GB.
PID: 394356; Command: bedtools; Return code: 0; Memory used: 0.592GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_minus_coverage.bed
(394913)Command completed. Elapsed time: 0:04:57. Running peak memory: 1.021GB.
PID: 394913; Command: bedtools; Return code: 0; Memory used: 0.475GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter Flanking Region
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_Flanking_Region
mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_Flanking_Region"
(395414)Command completed. Elapsed time: 0:00:00. Running peak memory: 1.021GB.
PID: 395414; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed
(395415,395416,395417,395418)Command completed. Elapsed time: 0:00:01. Running peak memory: 1.021GB.
PID: 395415; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 395417; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 395416; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 395418; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_Flanking_Region_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_Flanking_Region_plus_coverage.bed
(395421)Command completed. Elapsed time: 0:04:34. Running peak memory: 1.021GB.
PID: 395421; Command: bedtools; Return code: 0; Memory used: 0.098GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_Flanking_Region_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_Flanking_Region_minus_coverage.bed
(395977)Command completed. Elapsed time: 0:04:36. Running peak memory: 1.021GB.
PID: 395977; Command: bedtools; Return code: 0; Memory used: 0.166GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/5' UTR
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/5_UTR
mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/5_UTR"
(396492)Command completed. Elapsed time: 0:00:00. Running peak memory: 1.021GB.
PID: 396492; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/5_UTR_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/5_UTR_sort.bed
(396493,396494,396495,396496)Command completed. Elapsed time: 0:00:01. Running peak memory: 1.021GB.
PID: 396493; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 396494; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 396496; Command: bedtools; Return code: 0; Memory used: 0.01GB
PID: 396495; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_5_UTR_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_5_UTR_plus_coverage.bed
(396500)Command completed. Elapsed time: 0:04:30. Running peak memory: 1.021GB.
PID: 396500; Command: bedtools; Return code: 0; Memory used: 0.077GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_5_UTR_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_5_UTR_minus_coverage.bed
(414548)Command completed. Elapsed time: 0:04:12. Running peak memory: 1.021GB.
PID: 414548; Command: bedtools; Return code: 0; Memory used: 0.063GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/3' UTR
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/3_UTR
mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/3_UTR"
(419328)Command completed. Elapsed time: 0:00:00. Running peak memory: 1.021GB.
PID: 419328; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/3_UTR_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/3_UTR_sort.bed
(419329,419330,419331,419332)Command completed. Elapsed time: 0:00:01. Running peak memory: 1.021GB.
PID: 419329; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 419330; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 419332; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 419331; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_3_UTR_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_3_UTR_plus_coverage.bed
(419335)Command completed. Elapsed time: 0:04:40. Running peak memory: 1.021GB.
PID: 419335; Command: bedtools; Return code: 0; Memory used: 0.104GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_3_UTR_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_3_UTR_minus_coverage.bed
(419820)Command completed. Elapsed time: 0:04:35. Running peak memory: 1.021GB.
PID: 419820; Command: bedtools; Return code: 0; Memory used: 0.162GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Exon
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Exon_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Exon_sort.bed
(422032,422069,422085,422089)Command completed. Elapsed time: 0:00:03. Running peak memory: 1.021GB.
PID: 422032; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 422069; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 422089; Command: bedtools; Return code: 0; Memory used: 0.158GB
PID: 422085; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Exon_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Exon_plus_coverage.bed
(424370)Command completed. Elapsed time: 0:05:25. Running peak memory: 1.021GB.
PID: 424370; Command: bedtools; Return code: 0; Memory used: 0.468GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Exon_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Exon_minus_coverage.bed
(456033)Command completed. Elapsed time: 0:05:15. Running peak memory: 1.021GB.
PID: 456033; Command: bedtools; Return code: 0; Memory used: 0.186GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Intron
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Intron_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Intron_sort.bed
(29395,29396,29397,29398)Command completed. Elapsed time: 0:00:01. Running peak memory: 1.021GB.
PID: 29395; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 29397; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 29396; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 29398; Command: bedtools; Return code: 0; Memory used: 0.085GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Intron_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Intron_plus_coverage.bed
(29402)Command completed. Elapsed time: 0:06:15. Running peak memory: 1.021GB.
PID: 29402; Command: bedtools; Return code: 0; Memory used: 0.453GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Intron_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Intron_minus_coverage.bed
(57734)Command completed. Elapsed time: 0:06:21. Running peak memory: 1.021GB.
PID: 57734; Command: bedtools; Return code: 0; Memory used: 0.434GB
Plot cFRiF/FRiF (06-14 22:46:31) elapsed: 4139.0 TIME
samtools view -@ 32 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam
Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_cFRiF.pdf
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_PRO-seq_100 -z 3099922541 -n 192750289 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Intron_plus_coverage.bed
(80398)Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:46. Running peak memory: 1.021GB.
PID: 80398; Command: Rscript; Return code: 0; Memory used: 0.831GB
cFRiF
QC_hg38/K562_PRO-seq_100_cFRiF.pdf cFRiF QC_hg38/K562_PRO-seq_100_cFRiF.png PEPPRO OBJ Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_FRiF.pdf
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_PRO-seq_100 -z 3099922541 -n 192750289 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_Intron_plus_coverage.bed
(80459)Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:29. Running peak memory: 1.021GB.
PID: 80459; Command: Rscript; Return code: 0; Memory used: 0.439GB
FRiF
QC_hg38/K562_PRO-seq_100_FRiF.pdf FRiF QC_hg38/K562_PRO-seq_100_FRiF.png PEPPRO OBJ
Calculate mRNA contamination (06-14 22:48:18) elapsed: 106.0 TIME
Missing stat 'mRNA_contamination'
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_exons_sort.bed
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_introns_sort.bed
grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_exons.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_exons_sort.bed
(80502,80503)Command completed. Elapsed time: 0:00:05. Running peak memory: 1.021GB.
PID: 80503; Command: bedtools; Return code: 0; Memory used: 0.094GB
PID: 80502; Command: grep; Return code: 0; Memory used: 0.004GB
grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_introns.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_introns_sort.bed
(80512,80513,80514)Command completed. Elapsed time: 0:00:05. Running peak memory: 1.021GB.
PID: 80512; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 80514; Command: bedtools; Return code: 0; Memory used: 0.004GB
PID: 80513; Command: bedtools; Return code: 0; Memory used: 0.036GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exons_coverage.bed
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_introns_coverage.bed
bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exons_coverage.bed
(80522)Command completed. Elapsed time: 0:09:42. Running peak memory: 1.021GB.
PID: 80522; Command: bedtools; Return code: 0; Memory used: 0.293GB
bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_introns_coverage.bed
(131120)Command completed. Elapsed time: 0:13:29. Running peak memory: 1.021GB.
PID: 131120; Command: bedtools; Return code: 0; Memory used: 0.487GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_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]/387.328746)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exons_rpkm.bed
(193263,193271,193272)Command completed. Elapsed time: 0:00:01. Running peak memory: 1.021GB.
PID: 193263; Command: awk; Return code: 0; Memory used: 0.006GB
PID: 193272; Command: sort; Return code: 0; Memory used: 0.002GB
PID: 193271; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_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]/387.328746)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_introns_rpkm.bed
(193274,193275,193276)Command completed. Elapsed time: 0:00:01. Running peak memory: 1.021GB.
PID: 193274; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 193276; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 193275; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exon_intron_ratios.bed
join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exons_rpkm.bed | awk -v OFS=' ' 'NF==11 {print $7, $8, $9, $1, ($10/$5), $11}' | sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exon_intron_ratios.bed
(193279,193280,193281)Command completed. Elapsed time: 0:00:00. Running peak memory: 1.021GB.
PID: 193279; Command: join; Return code: 0; Memory used: 0.001GB
PID: 193281; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 193280; Command: awk; Return code: 0; Memory used: 0.001GB
awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exon_intron_ratios.bed | sort -n | awk ' { a[i++]=$1; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'
mRNA_contamination
1.37 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_mRNA_contamination.pdf
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exon_intron_ratios.bed --annotate
(193287)mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 1.021GB.
PID: 193287; Command: Rscript; Return code: 0; Memory used: 0.208GB
mRNA contamination
QC_hg38/K562_PRO-seq_100_mRNA_contamination.pdf mRNA contamination QC_hg38/K562_PRO-seq_100_mRNA_contamination.png PEPPRO OBJ Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exon_intron_ratios.bed.gz
pigz -f -p 32 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/QC_hg38/K562_PRO-seq_100_exon_intron_ratios.bed
(193318)Command completed. Elapsed time: 0:00:00. Running peak memory: 1.021GB.
PID: 193318; Command: pigz; Return code: 0; Memory used: 0.005GB
Produce bigWig files (06-14 23:11:46) elapsed: 1408.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_plus_exact_body_0-mer.bw
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_plus_smooth_body_0-mer.bw
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam
(193327)Command completed. Elapsed time: 0:03:00. Running peak memory: 1.021GB.
PID: 193327; Command: samtools; Return code: 0; Memory used: 0.019GB
/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_plus_smooth_body_0-mer.bw -p 21 --variable-step --tail-edge --scale 387328746.0
(193512)Cutting parallel chroms in half to accommodate two tracks. Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_plus.bam' Temporary files will be stored in: 'tmp_K562_PRO-seq_100_plus_cuttrace_l2uwmwym' Processing with 10 cores... stdin is empty of data stdin is empty of data stdin is empty of data Discarding 90 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270581v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1'] Keeping 105 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270538v1', 'chrUn_KI270580v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 105 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_plus_exact_body_0-mer.bw' Merging 105 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_plus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:08:30. Running peak memory: 3.847GB.
PID: 193512; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.847GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_minus_exact_body_0-mer.bw
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_minus_smooth_body_0-mer.bw
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam
(195542)Command completed. Elapsed time: 0:03:07. Running peak memory: 3.847GB.
PID: 195542; Command: samtools; Return code: 0; Memory used: 0.019GB
/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_minus_smooth_body_0-mer.bw -p 21 --variable-step --tail-edge --scale 387328746.0
(195934)Cutting parallel chroms in half to accommodate two tracks. Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/aligned_hg38/K562_PRO-seq_100_minus.bam' Temporary files will be stored in: 'tmp_K562_PRO-seq_100_minus_cuttrace_l74fklbt' Processing with 10 cores... stdin is empty of data psutil.NoSuchProcess process no longer exists (pid=195985) Warning: couldn't add memory use for process: 195934 stdin is empty of data stdin is empty of data stdin is empty of data stdin is empty of data psutil.NoSuchProcess process no longer exists (pid=196723) Warning: couldn't add memory use for process: 195934 Discarding 93 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr9_KI270717v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270593v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1'] Keeping 102 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270310v1', 'chrUn_KI270411v1', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270515v1', 'chrUn_KI270538v1', 'chrUn_KI270583v1', 'chrUn_KI270581v1', 'chrUn_KI270589v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270336v1', 'chrUn_KI270448v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 102 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_minus_exact_body_0-mer.bw' Merging 102 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_100/signal_hg38/K562_PRO-seq_100_minus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:08:09. Running peak memory: 4.216GB.
PID: 195934; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 4.216GB
Pipeline completed. Epilogue
- Elapsed time (this run): 2:23:44
- Total elapsed time (all runs): 13:29:45
- Peak memory (this run): 4.2155 GB
- Pipeline completed time: 2020-06-14 23:34:32