PEPPRO log - peppro

Pipeline run code and environment:

Command: /scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_treated_PRO-seq_3 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep3_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --input2 /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep3_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R
Compute host: udc-ba27-28c0
Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/
Pipeline started at: (06-15 07:17:18) elapsed: 1.0 TIME

Version log:

Python version: 3.6.6
Pypiper dir: /sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper
Pypiper version: 0.12.1
Pipeline dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines
Pipeline version: 0.9.8
Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
Pipeline branch: * master
Pipeline date: 2020-06-09 11:36:49 -0400
Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-)

Arguments passed to pipeline:

TSS_name: None
adapter: cutadapt
anno_name: None
complexity: False
config_file: peppro.yaml
cores: 12
coverage: False
dedup: seqkit
dirty: True
ensembl_gene_body: None
ensembl_tss: None
exon_name: None
force_follow: False
genome_assembly: hg38
input: ['/project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep3_PE1.fastq.gz']
input2: ['/project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep3_PE2.fastq.gz']
intron_name: None
keep: False
logdev: False
max_len: -1
mem: 12000
new_start: False
no_fifo: False
output_parent: /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline
paired_end: True
pre_name: None
prealignments: ['human_rDNA']
prioritize: False
protocol: PRO
recover: True
sample_name: H9_treated_PRO-seq_3
scale: True
search_file: None
silent: False
single_or_paired: PAIRED
sob: False
testmode: False
trimmer: seqtk
umi_len: 8
verbosity: None

Local input file: /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep3_PE1.fastq.gz Local input file: /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep3_PE2.fastq.gz

File_mb 2905.11 PEPPRO RES

Read_type PAIRED PEPPRO RES

Genome hg38 PEPPRO RES Detected PRO input

Merge/link and fastq conversion: (06-15 07:17:19) elapsed: 1.0 TIME

Number of input file sets: 2 Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R1.fastq.gz

ln -sf /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep3_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R1.fastq.gz (138710)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 138710; Command: ln; Return code: 0; Memory used: 0.0GB

Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R1.fastq.gz' Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R2.fastq.gz

ln -sf /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep3_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R2.fastq.gz (138713)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 138713; Command: ln; Return code: 0; Memory used: 0.0GB

Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R2.fastq.gz' Found .fastq.gz file Found .fastq.gz file Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1.fastq,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2.fastq

pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1.fastq (138720)
Command completed. Elapsed time: 0:02:52. Running peak memory: 0.002GB.
PID: 138720; Command: pigz; Return code: 0; Memory used: 0.002GB

pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2.fastq (54553)
Command completed. Elapsed time: 0:01:56. Running peak memory: 0.002GB.
PID: 54553; Command: pigz; Return code: 0; Memory used: 0.002GB

Raw_reads 120377388 PEPPRO RES

Fastq_reads 120377388 PEPPRO RES ['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/H9_treated_PRO-seq_3_R2.fastq.gz']

FASTQ processing: (06-15 07:25:41) elapsed: 502.0 TIME

cutadapt --version Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq

(cutadapt -j 12 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3_R1_cutadapt.txt (3572)
Command completed. Elapsed time: 0:02:51. Running peak memory: 4.399GB.
PID: 3572; Command: cutadapt; Return code: 0; Memory used: 4.399GB

seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq (3798,3799)
Command completed. Elapsed time: 0:00:51. Running peak memory: 4.399GB.
PID: 3798; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 3799; Command: seqtk; Return code: 0; Memory used: 0.002GB

Evaluating read trimming

Trimmed_reads 32320459 PEPPRO RES

Trim_loss_rate 73.15 PEPPRO RES Targetless command, running...

fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq (3889)
Started analysis of H9_treated_PRO-seq_3_R1_processed.fastq
Approx 5% complete for H9_treated_PRO-seq_3_R1_processed.fastq
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Analysis complete for H9_treated_PRO-seq_3_R1_processed.fastq
Command completed. Elapsed time: 0:01:03. Running peak memory: 4.399GB.
PID: 3889; Command: fastqc; Return code: 0; Memory used: 0.178GB

FastQC report r1 fastqc/H9_treated_PRO-seq_3_R1_processed_fastqc.html FastQC report r1 None PEPPRO OBJ Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_trimmed.fastq

seqkit rmdup --threads 12 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_noadap.fastq (4233)
[INFO][0m 4932446 duplicated records removed
Command completed. Elapsed time: 0:01:20. Running peak memory: 4.399GB.
PID: 4233; Command: seqkit; Return code: 0; Memory used: 2.046GB

seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_trimmed.fastq (4357,4358)
Command completed. Elapsed time: 0:00:46. Running peak memory: 4.399GB.
PID: 4357; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 4358; Command: seqtk; Return code: 0; Memory used: 0.002GB

grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3_R1_cutadapt.txt | awk '{print $(NF-1)}'

Reads_with_adapter 46004533.0 PEPPRO RES

grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3_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/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3_R1_cutadapt.txt

wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_short.fastq | awk '{print $1}'

Uninformative_adapter_reads 26667722.0 PEPPRO RES

Duplicate_reads 4932446.0 PEPPRO RES

Pct_uninformative_adapter_reads 44.3069 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/processed_R1.flag

touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/processed_R1.flag (4567)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.399GB.
PID: 4567; Command: touch; Return code: 0; Memory used: 0.002GB

cutadapt --version Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq

(cutadapt -j 12 -m 10 -O 1 -a GATCGTCGGACTGTAGAACTCTGAAC /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3_R2_cutadapt.txt (4570)
Command completed. Elapsed time: 0:02:00. Running peak memory: 4.399GB.
PID: 4570; Command: cutadapt; Return code: 0; Memory used: 3.415GB

seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq (4947,4948)
Command completed. Elapsed time: 0:00:50. Running peak memory: 4.399GB.
PID: 4947; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 4948; Command: seqtk; Return code: 0; Memory used: 0.002GB

Evaluating read trimming

Trimmed_reads 64640918 PEPPRO RES

Trim_loss_rate 46.3 PEPPRO RES Targetless command, running...

fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq (5051)
Started analysis of H9_treated_PRO-seq_3_R1_processed.fastq
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Analysis complete for H9_treated_PRO-seq_3_R1_processed.fastq
Command completed. Elapsed time: 0:01:02. Running peak memory: 4.399GB.
PID: 5051; Command: fastqc; Return code: 0; Memory used: 0.179GB

FastQC report r1 fastqc/H9_treated_PRO-seq_3_R1_processed_fastqc.html FastQC report r1 None PEPPRO OBJ Targetless command, running...

fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq (5140)
Started analysis of H9_treated_PRO-seq_3_R2_trimmed.fastq
Approx 5% complete for H9_treated_PRO-seq_3_R2_trimmed.fastq
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Analysis complete for H9_treated_PRO-seq_3_R2_trimmed.fastq
Command completed. Elapsed time: 0:01:19. Running peak memory: 4.399GB.
PID: 5140; Command: fastqc; Return code: 0; Memory used: 0.165GB

FastQC report r2 fastqc/H9_treated_PRO-seq_3_R2_trimmed_fastqc.html FastQC report r2 None PEPPRO OBJ Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3.hist,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3.histogram

fastq_pair -t 108339649 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_noadap.fastq (5227)
Left paired: 33366507       Right paired: 33366507
Left single: 154465     Right single: 1916320
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_noadap.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_noadap.fastq.single.fq
Command completed. Elapsed time: 0:04:36. Running peak memory: 7.355GB.
PID: 5227; Command: fastq_pair; Return code: 0; Memory used: 7.355GB

flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_noadap.fastq.paired.fq -o H9_treated_PRO-seq_3 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt (6033)
Command completed. Elapsed time: 0:01:22. Running peak memory: 7.355GB.
PID: 6033; Command: flash; Return code: 0; Memory used: 0.091GB

Plot adapter insertion distribution (06-15 07:45:31) elapsed: 1189.0 TIME

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3_adapter_insertion_distribution.pdf

Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R adapt -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt -u 8 (6460)
Adapter insertion distribution plot completed!

Command completed. Elapsed time: 0:00:06. Running peak memory: 7.355GB.
PID: 6460; Command: Rscript; Return code: 0; Memory used: 0.203GB

Adapter insertion distribution cutadapt/H9_treated_PRO-seq_3_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_treated_PRO-seq_3_adapter_insertion_distribution.png PEPPRO OBJ Missing stat 'Peak_adapter_insertion_size'

awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3.hist | awk 'BEGIN{max= 0; max_len=0; len=0}{if ($2>0+max) {max=$2; len=$1}; max_len=$1} END{print len-8}'

Peak_adapter_insertion_size 20 PEPPRO RES Missing stat 'Degradation_ratio'

Calculating degradation ratio (06-15 07:45:37) elapsed: 6.0 TIME

awk '{ if (($1-8) == 10) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3.hist

awk '{ if (($1-8) == 20) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3.hist

awk '{ if (($1-8) == 30) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3.hist

awk '{ if (($1-8) == 40) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3.hist

awk '(($1-8 ) <= 20 && ($1-8 ) >= 10){degradedSum += $2}; (($1-8 ) >= 30 && ($1-8) <= 40){intactSum += $2} END {if (intactSum < 1) {intactSum = 1} print degradedSum/intactSum}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/cutadapt/H9_treated_PRO-seq_3.hist

Degradation_ratio 0.9116 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed_dups.fastq

cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed_dups.fastq (6490)
Command completed. Elapsed time: 0:00:21. Running peak memory: 7.355GB.
PID: 6490; Command: cp; Return code: 0; Memory used: 0.002GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/processed_R2.flag

touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/processed_R2.flag (6516)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 6516; Command: touch; Return code: 0; Memory used: 0.0GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/repaired.flag

fastq_pair -t 108339649 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq (6517)
Left paired: 32136774       Right paired: 32136774
Left single: 183685     Right single: 1977423
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq.single.fq
Command completed. Elapsed time: 0:03:57. Running peak memory: 7.355GB.
PID: 6517; Command: fastq_pair; Return code: 0; Memory used: 7.13GB

mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq (6742)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 6742; Command: mv; Return code: 0; Memory used: 0.002GB

mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq (6743)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 6743; Command: mv; Return code: 0; Memory used: 0.001GB

touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/repaired.flag (6745)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 6745; Command: touch; Return code: 0; Memory used: 0.0GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/dups_repaired.flag

fastq_pair -t 108339649 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed_dups.fastq (6746)
Left paired: 27441885       Right paired: 27441885
Left single: 119928     Right single: 6672312
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed_dups.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed_dups.fastq.single.fq
Command completed. Elapsed time: 0:02:26. Running peak memory: 7.355GB.
PID: 6746; Command: fastq_pair; Return code: 0; Memory used: 5.969GB

mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_trimmed.fastq (7165)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 7165; Command: mv; Return code: 0; Memory used: 0.001GB

mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed_dups.fastq (7166)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 7166; Command: mv; Return code: 0; Memory used: 0.001GB

touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/dups_repaired.flag (7168)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 7168; Command: touch; Return code: 0; Memory used: 0.0GB

Prealignments (06-15 07:52:24) elapsed: 407.0 TIME

Prealignment assemblies: ['human_rDNA']

Map to human_rDNA (06-15 07:52:24) elapsed: 0.0 TIME

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/human_rDNA_bt2

mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/human_rDNA_bt2 (7169)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 7169; Command: mkfifo; Return code: 0; Memory used: 0.0GB

File not added to cleanup: prealignments/human_rDNA_bt2 Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R2.fq.gz

perl /scratch/jps3dp/tools/databio//peppro/tools/filter_paired_fq.pl /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R2.fq (7170)
(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id H9_treated_PRO-seq_3 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/human_rDNA_bt2 2>&1 > /dev/null) not gzipping output File not added to cleanup: prealignments/human_rDNA_bt2 Missing stat 'Aligned_reads_human_rDNA' 32136774 reads; of these: 32136774 (100.00%) were unpaired; of these: 28788351 (89.58%) aligned 0 times 3348423 (10.42%) aligned exactly 1 time 0 (0.00%) aligned >1 times 10.42% overall alignment rate

Aligned_reads_human_rDNA 6696846.0 PEPPRO RES

Alignment_rate_human_rDNA 10.36 PEPPRO RES

Map to human_rDNA (06-15 07:55:57) elapsed: 214.0 TIME

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/human_rDNA_dups_bt2

mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/human_rDNA_dups_bt2 (7602)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 7602; Command: mkfifo; Return code: 0; Memory used: 0.0GB

File not added to cleanup: prealignments/human_rDNA_dups_bt2 Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R2.fq.gz

perl /scratch/jps3dp/tools/databio//peppro/tools/filter_paired_fq.pl /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_dups_R2.fq (7603)
(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id H9_treated_PRO-seq_3 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/fastq/H9_treated_PRO-seq_3_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null) not gzipping output 3348423 reads skipped 0 reads lost File not added to cleanup: prealignments/human_rDNA_dups_bt2

Map to genome (06-15 07:59:20) elapsed: 203.0 TIME

No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_fail_qc_dups.bam Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort.bam

bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_treated_PRO-seq_3 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R2.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/tmpm93otle_ -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp.bam (7809,7810,7811)
2663663 reads skipped
0 reads lost
28788351 reads; of these:
  28788351 (100.00%) were paired; of these:
    12578156 (43.69%) aligned concordantly 0 times
    13526777 (46.99%) aligned concordantly exactly 1 time
    2683418 (9.32%) aligned concordantly >1 times
    ----
    12578156 pairs aligned concordantly 0 times; of these:
      3397179 (27.01%) aligned discordantly 1 time
    ----
    9180977 pairs aligned 0 times concordantly or discordantly; of these:
      18361954 mates make up the pairs; of these:
        7400125 (40.30%) aligned 0 times
        4038486 (21.99%) aligned exactly 1 time
        6923343 (37.70%) aligned >1 times
87.15% overall alignment rate
[bam_sort_core] merging from 16 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:48:46. Running peak memory: 7.355GB.
PID: 7810; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 7809; Command: bowtie2; Return code: 0; Memory used: 3.772GB
PID: 7811; Command: samtools; Return code: 0; Memory used: 0.895GB

samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort.bam (13121)
Command completed. Elapsed time: 0:01:35. Running peak memory: 7.355GB.
PID: 13121; Command: samtools; Return code: 0; Memory used: 0.018GB

samtools depth -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'

Mapped_reads 50176577 PEPPRO RES

QC_filtered_reads 29080016 PEPPRO RES

Aligned_reads 21096561.0 PEPPRO RES

Alignment_rate 32.64 PEPPRO RES

Total_efficiency 17.53 PEPPRO RES

Read_depth 3.98 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort_dups.bam

bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_treated_PRO-seq_3 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_dups_R2.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/tmpm93otle_ -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp_dups.bam (14710,14711,14712)
24778222 reads; of these:
  24778222 (100.00%) were paired; of these:
    10669067 (43.06%) aligned concordantly 0 times
    11790699 (47.58%) aligned concordantly exactly 1 time
    2318456 (9.36%) aligned concordantly >1 times
    ----
    10669067 pairs aligned concordantly 0 times; of these:
      2974174 (27.88%) aligned discordantly 1 time
    ----
    7694893 pairs aligned 0 times concordantly or discordantly; of these:
      15389786 mates make up the pairs; of these:
        6244577 (40.58%) aligned 0 times
        3533931 (22.96%) aligned exactly 1 time
        5611278 (36.46%) aligned >1 times
87.40% overall alignment rate
[bam_sort_core] merging from 14 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:42:51. Running peak memory: 7.355GB.
PID: 14710; Command: bowtie2; Return code: 0; Memory used: 3.758GB
PID: 14711; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 14712; Command: samtools; Return code: 0; Memory used: 0.895GB

samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort_dups.bam (18989)
Command completed. Elapsed time: 0:01:26. Running peak memory: 7.355GB.
PID: 18989; Command: samtools; Return code: 0; Memory used: 0.018GB

Compress all unmapped read files (06-15 09:46:12) elapsed: 6412.0 TIME

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R2.fq.gz

pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R2.fq (19314)
Command completed. Elapsed time: 0:00:25. Running peak memory: 7.355GB.
PID: 19314; Command: pigz; Return code: 0; Memory used: 0.009GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R1.fq.gz

pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/prealignments/H9_treated_PRO-seq_3_human_rDNA_unmap_R1.fq (19353)
Command completed. Elapsed time: 0:00:28. Running peak memory: 7.355GB.
PID: 19353; Command: pigz; Return code: 0; Memory used: 0.009GB

Missing stat 'Mitochondrial_reads' Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp.bam.bai

samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp.bam (19407)
Command completed. Elapsed time: 0:00:41. Running peak memory: 7.355GB.
PID: 19407; Command: samtools; Return code: 0; Memory used: 0.009GB

samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3

Mitochondrial_reads 667197 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_noMT.bam

samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort.bam (19473)
Command completed. Elapsed time: 0:00:31. Running peak memory: 7.355GB.
PID: 19473; Command: samtools; Return code: 0; Memory used: 0.011GB

samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_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/H9_treated_PRO-seq_3/aligned_hg38/chr_sizes.bed (19501,19502,19503,19504)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 19503; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 19501; Command: samtools; Return code: 0; Memory used: 0.006GB
PID: 19504; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 19502; Command: cut; Return code: 0; Memory used: 0.001GB

samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_noMT.bam (19506)
Command completed. Elapsed time: 0:00:39. Running peak memory: 7.355GB.
PID: 19506; Command: samtools; Return code: 0; Memory used: 0.019GB

mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort.bam (19559)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 19559; Command: mv; Return code: 0; Memory used: 0.002GB

samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort.bam (19560)
Command completed. Elapsed time: 0:00:32. Running peak memory: 7.355GB.
PID: 19560; Command: samtools; Return code: 0; Memory used: 0.01GB

Split BAM file (06-15 09:49:29) elapsed: 197.0 TIME

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE2.bam

samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam (19633,19634)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:53. Running peak memory: 7.355GB.
PID: 19633; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 19634; Command: samtools; Return code: 0; Memory used: 6.208GB

samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE2.bam (20143,20144)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:23. Running peak memory: 7.355GB.
PID: 20144; Command: samtools; Return code: 0; Memory used: 4.661GB
PID: 20143; Command: samtools; Return code: 0; Memory used: 0.004GB

Missing stat 'Maximum_read_length'

samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-

Maximum_read_length 38 PEPPRO RES Missing stat 'Genome_size'

awk '{sum+=$2} END {printf "%.0f", sum}' /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes

Genome_size 3099922541 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp_dups.bam.bai

samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp_dups.bam (20692)
Command completed. Elapsed time: 0:00:36. Running peak memory: 7.355GB.
PID: 20692; Command: samtools; Return code: 0; Memory used: 0.01GB

samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp_dups.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3 Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort_dups.bam
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort_dups.bam.bai Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_dups_PE1.bam,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_dups_PE2.bam

samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_dups_PE1.bam (20726,20727)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:36. Running peak memory: 7.355GB.
PID: 20726; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 20727; Command: samtools; Return code: 0; Memory used: 5.495GB

samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_dups_PE2.bam (20945,20946)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:07. Running peak memory: 7.355GB.
PID: 20945; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 20946; Command: samtools; Return code: 0; Memory used: 4.391GB

Calculate library complexity (06-15 10:01:09) elapsed: 700.0 TIME

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_out.txt

preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_dups_PE1.bam (21422)

BAM_INPUT TOTAL READS = 20168929 COUNTS_SUM = 20168929 DISTINCT READS = 1.4613e+07 DISTINCT COUNTS = 320 MAX COUNT = 14961 COUNTS OF 1 = 1.25301e+07 OBSERVED COUNTS (14962) 1 12530089 2 1265230 3 339731 4 151204 5 85421 6 54520 7 37501 8 26746 9 19937 10 15846 11 12083 12 9949 13 8065 14 6771 15 5607 16 4757 17 4010 18 3469 19 2981 20 2653 21 2307 22 1993 23 1854 24 1591 25 1387 26 1247 27 1131 28 985 29 895 30 810 31 746 32 697 33 666 34 606 35 568 36 521 37 480 38 454 39 380 40 365 41 350 42 333 43 308 44 273 45 240 46 229 47 211 48 234 49 223 50 197 51 159 52 172 53 144 54 136 55 128 56 137 57 129 58 129 59 122 60 112 61 86 62 95 63 83 64 99 65 73 66 77 67 71 68 63 69 73 70 69 71 60 72 57 73 57 74 50 75 66 76 49 77 41 78 48 79 42 80 39 81 31 82 43 83 43 84 45 85 34 86 32 87 36 88 34 89 21 90 24 91 31 92 34 93 30 94 27 95 31 96 19 97 24 98 17 99 24 100 19 101 19 102 18 103 12 104 25 105 15 106 13 107 15 108 19 109 17 110 16 111 14 112 13 113 15 114 14 115 9 116 17 117 10 118 16 119 18 120 14 121 10 122 12 123 18 124 6 125 9 126 8 127 10 128 7 129 5 130 6 131 8 132 11 133 6 134 10 135 9 136 5 137 6 138 8 139 2 140 8 141 7 142 4 143 3 144 7 145 7 146 6 147 10 148 9 149 5 150 8 151 4 152 7 153 5 154 1 155 8 156 3 157 3 158 4 159 7 160 2 161 7 162 4 163 5 164 5 165 2 166 2 167 3 168 4 169 4 170 1 171 4 172 4 173 2 174 5 175 2 176 1 177 3 178 2 179 1 180 4 181 1 182 1 183 5 184 2 185 3 186 2 187 3 188 4 189 2 190 1 191 4 192 2 193 2 196 3 197 4 199 2 200 1 201 2 202 1 203 1 204 1 205 1 206 1 207 1 209 1 210 2 211 1 212 1 213 3 214 3 215 2 216 3 217 1 218 1 219 1 222 2 223 1 224 1 225 1 226 1 229 1 230 1 231 4 232 3 233 1 237 2 238 2 239 2 241 1 242 1 244 3 246 1 247 1 251 2 254 2 255 3 256 3 259 2 260 1 262 1 264 2 265 1 268 2 269 1 270 1 271 1 273 1 276 1 278 3 280 1 284 1 289 1 291 3 295 1 302 1 303 1 305 2 306 1 308 1 309 1 311 1 314 2 315 2 319 1 325 2 328 1 329 1 330 1 340 2 342 1 343 1 346 1 347 1 355 1 377 1 378 1 379 1 389 1 390 1 396 1 400 1 404 1 405 1 406 1 410 1 416 1 421 1 426 1 427 1 432 1 441 1 453 1 454 1 459 1 461 1 504 1 512 1 514 1 551 1 598 1 606 1 646 1 686 1 693 1 727 1 736 1 792 1 858 1 903 1 951 1 1114 1 1290 1 1291 1 1482 1 1554 1 3863 1 4886 1 5882 1 12486 1 14961 1

sample size: 1000000 sample size: 2000000 sample size: 3000000 sample size: 4000000 sample size: 5000000 sample size: 6000000 sample size: 7000000 sample size: 8000000 sample size: 9000000 sample size: 10000000 sample size: 11000000 sample size: 12000000 sample size: 13000000 sample size: 14000000 sample size: 15000000 sample size: 16000000 sample size: 17000000 sample size: 18000000 sample size: 19000000 sample size: 20000000 Command completed. Elapsed time: 0:01:52. Running peak memory: 7.355GB.
PID: 21422; Command: preseq; Return code: 0; Memory used: 0.005GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_yield.txt

preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_dups_PE1.bam (21625)

BAM_INPUT TOTAL READS = 20168929 DISTINCT READS = 1.4613e+07 DISTINCT COUNTS = 320 MAX COUNT = 14961 COUNTS OF 1 = 1.25301e+07 MAX TERMS = 100 OBSERVED COUNTS (14962) 1 12530089 2 1265230 3 339731 4 151204 5 85421 6 54520 7 37501 8 26746 9 19937 10 15846 11 12083 12 9949 13 8065 14 6771 15 5607 16 4757 17 4010 18 3469 19 2981 20 2653 21 2307 22 1993 23 1854 24 1591 25 1387 26 1247 27 1131 28 985 29 895 30 810 31 746 32 697 33 666 34 606 35 568 36 521 37 480 38 454 39 380 40 365 41 350 42 333 43 308 44 273 45 240 46 229 47 211 48 234 49 223 50 197 51 159 52 172 53 144 54 136 55 128 56 137 57 129 58 129 59 122 60 112 61 86 62 95 63 83 64 99 65 73 66 77 67 71 68 63 69 73 70 69 71 60 72 57 73 57 74 50 75 66 76 49 77 41 78 48 79 42 80 39 81 31 82 43 83 43 84 45 85 34 86 32 87 36 88 34 89 21 90 24 91 31 92 34 93 30 94 27 95 31 96 19 97 24 98 17 99 24 100 19 101 19 102 18 103 12 104 25 105 15 106 13 107 15 108 19 109 17 110 16 111 14 112 13 113 15 114 14 115 9 116 17 117 10 118 16 119 18 120 14 121 10 122 12 123 18 124 6 125 9 126 8 127 10 128 7 129 5 130 6 131 8 132 11 133 6 134 10 135 9 136 5 137 6 138 8 139 2 140 8 141 7 142 4 143 3 144 7 145 7 146 6 147 10 148 9 149 5 150 8 151 4 152 7 153 5 154 1 155 8 156 3 157 3 158 4 159 7 160 2 161 7 162 4 163 5 164 5 165 2 166 2 167 3 168 4 169 4 170 1 171 4 172 4 173 2 174 5 175 2 176 1 177 3 178 2 179 1 180 4 181 1 182 1 183 5 184 2 185 3 186 2 187 3 188 4 189 2 190 1 191 4 192 2 193 2 196 3 197 4 199 2 200 1 201 2 202 1 203 1 204 1 205 1 206 1 207 1 209 1 210 2 211 1 212 1 213 3 214 3 215 2 216 3 217 1 218 1 219 1 222 2 223 1 224 1 225 1 226 1 229 1 230 1 231 4 232 3 233 1 237 2 238 2 239 2 241 1 242 1 244 3 246 1 247 1 251 2 254 2 255 3 256 3 259 2 260 1 262 1 264 2 265 1 268 2 269 1 270 1 271 1 273 1 276 1 278 3 280 1 284 1 289 1 291 3 295 1 302 1 303 1 305 2 306 1 308 1 309 1 311 1 314 2 315 2 319 1 325 2 328 1 329 1 330 1 340 2 342 1 343 1 346 1 347 1 355 1 377 1 378 1 379 1 389 1 390 1 396 1 400 1 404 1 405 1 406 1 410 1 416 1 421 1 426 1 427 1 432 1 441 1 453 1 454 1 459 1 461 1 504 1 512 1 514 1 551 1 598 1 606 1 646 1 686 1 693 1 727 1 736 1 792 1 858 1 903 1 951 1 1114 1 1290 1 1291 1 1482 1 1554 1 3863 1 4886 1 5882 1 12486 1 14961 1

[ESTIMATING YIELD CURVE] [BOOTSTRAPPING HISTOGRAM] ..............................................................................................._..... [COMPUTING CONFIDENCE INTERVALS] [WRITING OUTPUT] Command completed. Elapsed time: 0:01:57. Running peak memory: 7.355GB.
PID: 21625; Command: preseq; Return code: 0; Memory used: 0.005GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_counts.txt

echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_counts.txt (21786)
Command completed. Elapsed time: 0:00:31. Running peak memory: 7.355GB.
PID: 21786; Command: echo; Return code: 0; Memory used: 0.006GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_plot.pdf,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_plot.png

Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R preseq -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_plot (22074)
Processing H9_treated_PRO-seq_3
INFO: Found real counts for H9_treated_PRO-seq_3 - Total (M): 22.825749 Unique (M): 20.168929

Library complexity plot completed!

Command completed. Elapsed time: 0:00:05. Running peak memory: 7.355GB.
PID: 22074; Command: Rscript; Return code: 0; Memory used: 0.316GB

Library complexity QC_hg38/H9_treated_PRO-seq_3_preseq_plot.pdf Library complexity QC_hg38/H9_treated_PRO-seq_3_preseq_plot.png PEPPRO OBJ Missing stat 'Frac_exp_unique_at_10M'

grep -w '10000000' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_preseq_yield.txt | awk '{print $2}'

Frac_exp_unique_at_10M 0.7916 PEPPRO RES

Calculate NRF, PBC1, and PBC2 (06-15 10:05:33) elapsed: 264.0 TIME

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam.bai

samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam (22092)
Command completed. Elapsed time: 0:00:17. Running peak memory: 7.355GB.
PID: 22092; Command: samtools; Return code: 0; Memory used: 0.015GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_bamQC.tsv

/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_bamQC.tsv (22112)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/tmp_H9_treated_PRO-seq_3_PE1_89bj3hev'
Processing with 12 cores...
Discarding 98 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', '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_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270752v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1']
Keeping 97 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', 'chr2_KI270716v1_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', 'chr22_KI270739v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270584v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Command completed. Elapsed time: 0:00:24. Running peak memory: 7.355GB.
PID: 22112; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 2.007GB

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/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_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/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_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/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_bamQC.tsv

NRF 1.0 PEPPRO RES

PBC1 11412874.5 PEPPRO RES

PBC2 11412874.5 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_unmap.bam

samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_unmap.bam (22208)
Command completed. Elapsed time: 0:00:10. Running peak memory: 7.355GB.
PID: 22208; Command: samtools; Return code: 0; Memory used: 0.009GB

samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_temp.bam

Unmapped_reads 7400125 PEPPRO RES

Split BAM by strand (06-15 10:06:33) elapsed: 60.0 TIME

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam

samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam (22277)
Command completed. Elapsed time: 0:01:17. Running peak memory: 7.355GB.
PID: 22277; Command: samtools; Return code: 0; Memory used: 0.006GB

samtools view -bh -f 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam (22436)
Command completed. Elapsed time: 0:01:15. Running peak memory: 7.355GB.
PID: 22436; Command: samtools; Return code: 0; Memory used: 0.006GB

Calculate TSS enrichment (06-15 10:09:05) elapsed: 152.0 TIME

Missing stat 'TSS_non-coding_score' Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/plus_TSS.tsv,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/minus_TSS.tsv

sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed (22531)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 22531; Command: sed; Return code: 0; Memory used: 0.001GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_plus_TssEnrichment.txt

/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_plus_TssEnrichment.txt (22532)
Command completed. Elapsed time: 0:00:08. Running peak memory: 7.355GB.
PID: 22532; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.702GB

TSS_coding_score 60.1 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_minus_TssEnrichment.txt

/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_minus_TssEnrichment.txt (22565)
Command completed. Elapsed time: 0:00:06. Running peak memory: 7.355GB.
PID: 22565; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.767GB

TSS_non-coding_score 17.8 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_TSSenrichment.pdf

Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_minus_TssEnrichment.txt (22599)

Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_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: 0:00:06. Running peak memory: 7.355GB.
PID: 22599; Command: Rscript; Return code: 0; Memory used: 0.316GB

TSS enrichment QC_hg38/H9_treated_PRO-seq_3_TSSenrichment.pdf TSS enrichment QC_hg38/H9_treated_PRO-seq_3_TSSenrichment.png PEPPRO OBJ Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt

samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.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/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt (22622,22623,22624,22625)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 22622; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 22624; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 22623; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 22625; Command: awk; Return code: 0; Memory used: 0.0GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_keep.txt

cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_keep.txt (22627)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 22627; Command: cut; Return code: 0; Memory used: 0.0GB

Calculate Pause Index (PI) (06-15 10:09:26) elapsed: 21.0 TIME

Missing stat 'Pause_index' Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_ensembl_tss.bed,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_ensembl_gene_body.bed

grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/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/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_ensembl_tss.bed (22629,22630)
Command completed. Elapsed time: 0:00:02. Running peak memory: 7.355GB.
PID: 22629; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 22630; Command: bedtools; Return code: 0; Memory used: 0.093GB

grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/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/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_ensembl_gene_body.bed (22633,22634)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 22633; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 22634; Command: bedtools; Return code: 0; Memory used: 0.005GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_TSS_density.bed

bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/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/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_TSS_density.bed (22636,22637,22638,22639)
Command completed. Elapsed time: 0:00:31. Running peak memory: 7.355GB.
PID: 22637; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 22639; Command: sort; Return code: 0; Memory used: 0.002GB
PID: 22636; Command: bedtools; Return code: 0; Memory used: 0.01GB
PID: 22638; Command: sort; Return code: 0; Memory used: 0.004GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_gene_body_density.bed

bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_gene_body_density.bed (22766,22767,22768)
Command completed. Elapsed time: 0:00:36. Running peak memory: 7.355GB.
PID: 22768; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 22766; Command: bedtools; Return code: 0; Memory used: 0.057GB
PID: 22767; Command: awk; Return code: 0; Memory used: 0.001GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_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/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_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/H9_treated_PRO-seq_3/QC_hg38/tmpq0v5ymlg (23104,23105,23106)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 23104; Command: join; Return code: 0; Memory used: 0.001GB
PID: 23106; Command: env; Return code: 0; Memory used: 0.004GB
PID: 23105; Command: awk; Return code: 0; Memory used: 0.001GB

awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/tmpq0v5ymlg | 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/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_pause_index.bed

awk -v OFS=' ' '{ if ($5 > 0.0223084) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/tmpq0v5ymlg > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_pause_index.bed (23112)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 23112; Command: awk; Return code: 0; Memory used: 0.002GB

sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_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 63.1 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_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/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_pause_index.bed (23117)
Pause index plot completed!

Command completed. Elapsed time: 0:00:04. Running peak memory: 7.355GB.
PID: 23117; Command: Rscript; Return code: 0; Memory used: 0.317GB

Pause index QC_hg38/H9_treated_PRO-seq_3_pause_index.pdf Pause index QC_hg38/H9_treated_PRO-seq_3_pause_index.png PEPPRO OBJ Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_pause_index.bed.gz

pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_pause_index.bed (23138)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 23138; Command: pigz; Return code: 0; Memory used: 0.002GB

Calculate Fraction of Reads in pre-mature mRNA (06-15 10:10:40) elapsed: 74.0 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/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam 21096561.0 8414821

Plus_FRiP 0.4 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/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam 21096561.0 7977228

Minus_FRiP 0.38 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_gene_coverage.bed

grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/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/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_gene_sort.bed (23249,23250)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 23249; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 23250; Command: bedtools; Return code: 0; Memory used: 0.006GB

bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_gene_coverage.bed (23252)
Command completed. Elapsed time: 0:00:35. Running peak memory: 7.355GB.
PID: 23252; Command: bedtools; Return code: 0; Memory used: 0.06GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/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/H9_treated_PRO-seq_3/raw/hg38_annotations.bed.gz (23297)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 23297; Command: ln; Return code: 0; Memory used: 0.0GB

pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/hg38_annotations.bed (23298)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 23298; Command: pigz; Return code: 0; Memory used: 0.002GB

Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 10:11:57) elapsed: 77.0 TIME

cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/hg38_annotations.bed | sort -u Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Enhancer

awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/raw/hg38_annotations.bed (23308)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 23308; Command: awk; Return code: 0; Memory used: 0.002GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Enhancer_sort.bed

cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Enhancer_sort.bed (23310,23311,23312,23313)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 23310; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23311; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 23313; Command: bedtools; Return code: 0; Memory used: 0.012GB
PID: 23312; Command: cut; Return code: 0; Memory used: 0.001GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Enhancer_plus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Enhancer_plus_coverage.bed (23316)
Command completed. Elapsed time: 0:00:14. Running peak memory: 7.355GB.
PID: 23316; Command: bedtools; Return code: 0; Memory used: 0.008GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Enhancer_minus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Enhancer_minus_coverage.bed (23349)
Command completed. Elapsed time: 0:00:14. Running peak memory: 7.355GB.
PID: 23349; Command: bedtools; Return code: 0; Memory used: 0.01GB

Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_sort.bed

cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_sort.bed (23365,23366,23367,23368)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 23365; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23366; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 23368; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 23367; Command: cut; Return code: 0; Memory used: 0.001GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_plus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_plus_coverage.bed (23370)
Command completed. Elapsed time: 0:00:16. Running peak memory: 7.355GB.
PID: 23370; Command: bedtools; Return code: 0; Memory used: 0.023GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_minus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_minus_coverage.bed (23433)
Command completed. Elapsed time: 0:00:15. Running peak memory: 7.355GB.
PID: 23433; Command: bedtools; Return code: 0; Memory used: 0.025GB

Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter Flanking Region
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_Flanking_Region

mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_Flanking_Region" (23508)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 23508; Command: mv; Return code: 0; Memory used: 0.0GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_Flanking_Region_sort.bed

cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_Flanking_Region_sort.bed (23509,23510,23511,23512)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 23509; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23511; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 23510; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 23512; Command: bedtools; Return code: 0; Memory used: 0.009GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_Flanking_Region_plus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_Flanking_Region_plus_coverage.bed (23514)
Command completed. Elapsed time: 0:00:15. Running peak memory: 7.355GB.
PID: 23514; Command: bedtools; Return code: 0; Memory used: 0.011GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_Flanking_Region_minus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_Flanking_Region_minus_coverage.bed (23545)
Command completed. Elapsed time: 0:00:14. Running peak memory: 7.355GB.
PID: 23545; Command: bedtools; Return code: 0; Memory used: 0.013GB

Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/5' UTR
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/5_UTR

mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/5_UTR" (23572)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 23572; Command: mv; Return code: 0; Memory used: 0.002GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/5_UTR_sort.bed

cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/5_UTR_sort.bed (23573,23574,23575,23576)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 23573; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23574; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 23576; Command: bedtools; Return code: 0; Memory used: 0.011GB
PID: 23575; Command: cut; Return code: 0; Memory used: 0.001GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_5_UTR_plus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_5_UTR_plus_coverage.bed (23578)
Command completed. Elapsed time: 0:00:15. Running peak memory: 7.355GB.
PID: 23578; Command: bedtools; Return code: 0; Memory used: 0.012GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_5_UTR_minus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_5_UTR_minus_coverage.bed (23627)
Command completed. Elapsed time: 0:00:14. Running peak memory: 7.355GB.
PID: 23627; Command: bedtools; Return code: 0; Memory used: 0.015GB

Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/3' UTR
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/3_UTR

mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/3_UTR" (23669)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 23669; Command: mv; Return code: 0; Memory used: 0.0GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/3_UTR_sort.bed

cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/3_UTR_sort.bed (23670,23671,23672,23673)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 23670; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23671; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 23673; Command: bedtools; Return code: 0; Memory used: 0.011GB
PID: 23672; Command: cut; Return code: 0; Memory used: 0.001GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_3_UTR_plus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_3_UTR_plus_coverage.bed (23675)
Command completed. Elapsed time: 0:00:15. Running peak memory: 7.355GB.
PID: 23675; Command: bedtools; Return code: 0; Memory used: 0.013GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_3_UTR_minus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_3_UTR_minus_coverage.bed (23701)
Command completed. Elapsed time: 0:00:14. Running peak memory: 7.355GB.
PID: 23701; Command: bedtools; Return code: 0; Memory used: 0.011GB

Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Exon
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Exon_sort.bed

cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Exon_sort.bed (23739,23740,23741,23742)
Command completed. Elapsed time: 0:00:03. Running peak memory: 7.355GB.
PID: 23739; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23740; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 23742; Command: bedtools; Return code: 0; Memory used: 0.158GB
PID: 23741; Command: cut; Return code: 0; Memory used: 0.001GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Exon_plus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Exon_plus_coverage.bed (23746)
Command completed. Elapsed time: 0:00:16. Running peak memory: 7.355GB.
PID: 23746; Command: bedtools; Return code: 0; Memory used: 0.025GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Exon_minus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Exon_minus_coverage.bed (23782)
Command completed. Elapsed time: 0:00:16. Running peak memory: 7.355GB.
PID: 23782; Command: bedtools; Return code: 0; Memory used: 0.019GB

Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Intron
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Intron_sort.bed

cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Intron_sort.bed (23995,23996,23997,23998)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 23995; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23997; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 23996; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 23998; Command: bedtools; Return code: 0; Memory used: 0.077GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Intron_plus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Intron_plus_coverage.bed (24046)
Command completed. Elapsed time: 0:00:17. Running peak memory: 7.355GB.
PID: 24046; Command: bedtools; Return code: 0; Memory used: 0.058GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Intron_minus_coverage.bed

bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Intron_minus_coverage.bed (24598)
Command completed. Elapsed time: 0:00:17. Running peak memory: 7.355GB.
PID: 24598; Command: bedtools; Return code: 0; Memory used: 0.037GB

Plot cFRiF/FRiF (06-15 10:15:40) elapsed: 222.0 TIME

samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_cFRiF.pdf

Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_treated_PRO-seq_3 -z 3099922541 -n 11561442 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Intron_plus_coverage.bed (24663)
Cumulative cfrif plot completed!

Command completed. Elapsed time: 0:00:36. Running peak memory: 7.355GB.
PID: 24663; Command: Rscript; Return code: 0; Memory used: 0.44GB

cFRiF QC_hg38/H9_treated_PRO-seq_3_cFRiF.pdf cFRiF QC_hg38/H9_treated_PRO-seq_3_cFRiF.png PEPPRO OBJ Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_FRiF.pdf

Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_treated_PRO-seq_3 -z 3099922541 -n 11561442 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_Intron_plus_coverage.bed (24726)
Cumulative frif plot completed!

Command completed. Elapsed time: 0:00:26. Running peak memory: 7.355GB.
PID: 24726; Command: Rscript; Return code: 0; Memory used: 0.448GB

FRiF QC_hg38/H9_treated_PRO-seq_3_FRiF.pdf FRiF QC_hg38/H9_treated_PRO-seq_3_FRiF.png PEPPRO OBJ

Calculate mRNA contamination (06-15 10:16:43) elapsed: 64.0 TIME

Missing stat 'mRNA_contamination' Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_exons_sort.bed,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_introns_sort.bed

grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/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/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_exons_sort.bed (24785,24786)
Command completed. Elapsed time: 0:00:05. Running peak memory: 7.355GB.
PID: 24786; Command: bedtools; Return code: 0; Memory used: 0.089GB
PID: 24785; Command: grep; Return code: 0; Memory used: 0.004GB

grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/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/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_introns_sort.bed (24794,24795,24796)
Command completed. Elapsed time: 0:00:05. Running peak memory: 7.355GB.
PID: 24794; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 24796; Command: bedtools; Return code: 0; Memory used: 0.007GB
PID: 24795; Command: bedtools; Return code: 0; Memory used: 0.033GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exons_coverage.bed,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_introns_coverage.bed

bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exons_coverage.bed (24802)
Command completed. Elapsed time: 0:00:28. Running peak memory: 7.355GB.
PID: 24802; Command: bedtools; Return code: 0; Memory used: 0.012GB

bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_introns_coverage.bed (24831)
Command completed. Elapsed time: 0:00:33. Running peak memory: 7.355GB.
PID: 24831; Command: bedtools; Return code: 0; Memory used: 0.036GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exons_rpkm.bed

awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/21.096561)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exons_rpkm.bed (24968,24969,24970)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 24968; Command: awk; Return code: 0; Memory used: 0.009GB
PID: 24970; Command: sort; Return code: 0; Memory used: 0.002GB
PID: 24969; Command: awk; Return code: 0; Memory used: 0.001GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_introns_rpkm.bed

awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/21.096561)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_introns_rpkm.bed (24972,24973,24974)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.355GB.
PID: 24972; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 24974; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 24973; Command: awk; Return code: 0; Memory used: 0.001GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exon_intron_ratios.bed

join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_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/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exon_intron_ratios.bed (24977,24978,24979)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 24977; Command: join; Return code: 0; Memory used: 0.001GB
PID: 24979; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 24978; Command: awk; Return code: 0; Memory used: 0.001GB

awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_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 1.1 PEPPRO RES Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_mRNA_contamination.pdf

Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exon_intron_ratios.bed --annotate (24985)
mRNA contamination plot completed!

Command completed. Elapsed time: 0:00:05. Running peak memory: 7.355GB.
PID: 24985; Command: Rscript; Return code: 0; Memory used: 0.316GB

mRNA contamination QC_hg38/H9_treated_PRO-seq_3_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_treated_PRO-seq_3_mRNA_contamination.png PEPPRO OBJ Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exon_intron_ratios.bed.gz

pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/QC_hg38/H9_treated_PRO-seq_3_exon_intron_ratios.bed (25006)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.355GB.
PID: 25006; Command: pigz; Return code: 0; Memory used: 0.003GB

Produce bigWig files (06-15 10:18:01) elapsed: 78.0 TIME

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_plus_exact_body_0-mer.bw,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_plus_smooth_body_0-mer.bw

samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam (25014)

Command completed. Elapsed time: 0:00:09. Running peak memory: 7.355GB.
PID: 25014; Command: samtools; Return code: 0; Memory used: 0.009GB

/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 21096561.0 (25022)

Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_plus.bam'
Temporary files will be stored in: 'tmp_H9_treated_PRO-seq_3_plus_cuttrace_mrjp2wis'
Processing with 4 cores...
stdin is empty of data
stdin is empty of data
Discarding 114 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr22_KI270735v1_random', 'chr22_KI270737v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270743v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1']
Keeping 81 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_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_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_KI270736v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270744v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 81 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_plus_exact_body_0-mer.bw'
Merging 81 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_plus_smooth_body_0-mer.bw'

Command completed. Elapsed time: 0:07:31. Running peak memory: 7.355GB.
PID: 25022; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.735GB

Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_minus_exact_body_0-mer.bw,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_minus_smooth_body_0-mer.bw

samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam (28234)

Command completed. Elapsed time: 0:00:09. Running peak memory: 7.355GB.
PID: 28234; Command: samtools; Return code: 0; Memory used: 0.009GB

/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 21096561.0 (28252)

Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/aligned_hg38/H9_treated_PRO-seq_3_minus.bam'
Temporary files will be stored in: 'tmp_H9_treated_PRO-seq_3_minus_cuttrace_5fa0aciy'
Processing with 4 cores...
Discarding 109 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', '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_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1']
Keeping 86 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270708v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_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_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270589v1', 'chrUn_KI270584v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', '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_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 86 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_minus_exact_body_0-mer.bw'
Merging 86 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_3/signal_hg38/H9_treated_PRO-seq_3_minus_smooth_body_0-mer.bw'

Command completed. Elapsed time: 0:07:35. Running peak memory: 7.355GB.
PID: 28252; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.754GB

Pipeline completed. Epilogue

Elapsed time (this run): 3:16:06
Total elapsed time (all runs): 5:45:59
Peak memory (this run): 7.3549 GB
Pipeline completed time: 2020-06-15 10:33:24

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