Pipeline run code and environment:
- Command:
/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_treated_PRO-seq_2 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep2_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_rep2_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_2/
- 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_rep2_PE1.fastq.gz']
input2
:['/project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep2_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_2
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_rep2_PE1.fastq.gz Local input file: /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep2_PE2.fastq.gz
File_mb
2737.32 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_2/raw/H9_treated_PRO-seq_2_R1.fastq.gz
ln -sf /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep2_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/raw/H9_treated_PRO-seq_2_R1.fastq.gz
(138709)Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 138709; 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_2/raw/H9_treated_PRO-seq_2_R1.fastq.gz'
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/raw/H9_treated_PRO-seq_2_R2.fastq.gz
ln -sf /project/shefflab/data//guertin/fastq/H9_200nM_romidepsin_rep2_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/raw/H9_treated_PRO-seq_2_R2.fastq.gz
(138712)Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 138712; 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_2/raw/H9_treated_PRO-seq_2_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_2/fastq/H9_treated_PRO-seq_2_R1.fastq
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2.fastq
pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/raw/H9_treated_PRO-seq_2_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1.fastq
(138715)Command completed. Elapsed time: 0:02:49. Running peak memory: 0.002GB.
PID: 138715; 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_2/raw/H9_treated_PRO-seq_2_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2.fastq
(45196)Command completed. Elapsed time: 0:01:47. Running peak memory: 0.002GB.
PID: 45196; Command: pigz; Return code: 0; Memory used: 0.002GB
Raw_reads
114083518 PEPPRO RES
Fastq_reads
114083518 PEPPRO RES ['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/raw/H9_treated_PRO-seq_2_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/raw/H9_treated_PRO-seq_2_R2.fastq.gz']
FASTQ processing: (06-15 07:25:43) elapsed: 504.0 TIME
cutadapt --version
Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_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_2/fastq/H9_treated_PRO-seq_2_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/cutadapt/H9_treated_PRO-seq_2_R1_cutadapt.txt
(3602)Command completed. Elapsed time: 0:02:40. Running peak memory: 3.232GB.
PID: 3602; Command: cutadapt; Return code: 0; Memory used: 3.232GB
seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq
(3786,3787)Command completed. Elapsed time: 0:00:39. Running peak memory: 3.232GB.
PID: 3786; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 3787; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
Trimmed_reads
28674037 PEPPRO RES
Trim_loss_rate
74.87 PEPPRO RES Targetless command, running...
fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq
(3848)Started analysis of H9_treated_PRO-seq_2_R1_processed.fastq Approx 5% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 10% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 15% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 20% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 25% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 30% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 35% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 40% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 45% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 50% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 55% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 60% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 65% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 70% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 75% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 80% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 85% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 90% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 95% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 100% complete for H9_treated_PRO-seq_2_R1_processed.fastq Analysis complete for H9_treated_PRO-seq_2_R1_processed.fastqCommand completed. Elapsed time: 0:00:58. Running peak memory: 3.232GB.
PID: 3848; Command: fastqc; Return code: 0; Memory used: 0.182GB
FastQC report r1
fastqc/H9_treated_PRO-seq_2_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_2/fastq/H9_treated_PRO-seq_2_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_2/fastq/H9_treated_PRO-seq_2_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_noadap.fastq
(3943)[INFO][0m 2388789 duplicated records removedCommand completed. Elapsed time: 0:01:04. Running peak memory: 3.232GB.
PID: 3943; Command: seqkit; Return code: 0; Memory used: 2.036GB
seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_trimmed.fastq
(4301,4302)Command completed. Elapsed time: 0:00:37. Running peak memory: 3.232GB.
PID: 4301; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 4302; 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_2/cutadapt/H9_treated_PRO-seq_2_R1_cutadapt.txt | awk '{print $(NF-1)}'
Reads_with_adapter
43984199.0 PEPPRO RES
grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/cutadapt/H9_treated_PRO-seq_2_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_2/cutadapt/H9_treated_PRO-seq_2_R1_cutadapt.txt
wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_short.fastq | awk '{print $1}'
Uninformative_adapter_reads
27614116.0 PEPPRO RES
Duplicate_reads
2388789.0 PEPPRO RES
Pct_uninformative_adapter_reads
48.4104 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/processed_R1.flag
touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/processed_R1.flag
(4515)Command completed. Elapsed time: 0:00:00. Running peak memory: 3.232GB.
PID: 4515; Command: touch; Return code: 0; Memory used: 0.0GB
cutadapt --version
Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_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_2/fastq/H9_treated_PRO-seq_2_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/cutadapt/H9_treated_PRO-seq_2_R2_cutadapt.txt
(4517)Command completed. Elapsed time: 0:02:10. Running peak memory: 3.35GB.
PID: 4517; Command: cutadapt; Return code: 0; Memory used: 3.35GB
seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed.fastq
(4928,4929)Command completed. Elapsed time: 0:00:47. Running peak memory: 3.35GB.
PID: 4928; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 4929; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
Trimmed_reads
57348074 PEPPRO RES
Trim_loss_rate
49.73 PEPPRO RES Targetless command, running...
fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq
(5021)Started analysis of H9_treated_PRO-seq_2_R1_processed.fastq Approx 5% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 10% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 15% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 20% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 25% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 30% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 35% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 40% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 45% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 50% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 55% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 60% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 65% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 70% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 75% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 80% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 85% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 90% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 95% complete for H9_treated_PRO-seq_2_R1_processed.fastq Approx 100% complete for H9_treated_PRO-seq_2_R1_processed.fastq Analysis complete for H9_treated_PRO-seq_2_R1_processed.fastqCommand completed. Elapsed time: 0:00:59. Running peak memory: 3.35GB.
PID: 5021; Command: fastqc; Return code: 0; Memory used: 0.179GB
FastQC report r1
fastqc/H9_treated_PRO-seq_2_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_2/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed.fastq
(5107)Started analysis of H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 5% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 10% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 15% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 20% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 25% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 30% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 35% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 40% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 45% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 50% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 55% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 60% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 65% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 70% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 75% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 80% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 85% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 90% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Approx 95% complete for H9_treated_PRO-seq_2_R2_trimmed.fastq Analysis complete for H9_treated_PRO-seq_2_R2_trimmed.fastqCommand completed. Elapsed time: 0:01:03. Running peak memory: 3.35GB.
PID: 5107; Command: fastqc; Return code: 0; Memory used: 0.17GB
FastQC report r2
fastqc/H9_treated_PRO-seq_2_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_2/cutadapt/H9_treated_PRO-seq_2.hist
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/cutadapt/H9_treated_PRO-seq_2.histogram
fastq_pair -t 102675166 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_noadap.fastq
(5194)Left paired: 29252476 Right paired: 29252476 Left single: 175167 Right single: 2238349 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_noadap.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_noadap.fastq.single.fqCommand completed. Elapsed time: 0:04:07. Running peak memory: 6.557GB.
PID: 5194; Command: fastq_pair; Return code: 0; Memory used: 6.557GB
flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_noadap.fastq.paired.fq -o H9_treated_PRO-seq_2 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/cutadapt
(5825)Command completed. Elapsed time: 0:01:04. Running peak memory: 6.557GB.
PID: 5825; Command: flash; Return code: 0; Memory used: 0.117GB
Plot adapter insertion distribution (06-15 07:44:09) elapsed: 1106.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/cutadapt/H9_treated_PRO-seq_2_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_2/cutadapt/H9_treated_PRO-seq_2.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/cutadapt -u 8
(6026)Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 6.557GB.
PID: 6026; Command: Rscript; Return code: 0; Memory used: 0.204GB
Adapter insertion distribution
cutadapt/H9_treated_PRO-seq_2_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_treated_PRO-seq_2_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_2/cutadapt/H9_treated_PRO-seq_2.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 07:44:15) 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_2/cutadapt/H9_treated_PRO-seq_2.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_2/cutadapt/H9_treated_PRO-seq_2.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_2/cutadapt/H9_treated_PRO-seq_2.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_2/cutadapt/H9_treated_PRO-seq_2.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_2/cutadapt/H9_treated_PRO-seq_2.hist
Degradation_ratio
1.0037 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed_dups.fastq
cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed_dups.fastq
(6203)Command completed. Elapsed time: 0:00:34. Running peak memory: 6.557GB.
PID: 6203; 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_2/fastq/processed_R2.flag
touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/processed_R2.flag
(6234)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 6234; 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_2/fastq/repaired.flag
fastq_pair -t 102675166 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed.fastq
(6235)Left paired: 28465823 Right paired: 28465823 Left single: 208214 Right single: 2295865 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed.fastq.single.fqCommand completed. Elapsed time: 0:02:40. Running peak memory: 6.557GB.
PID: 6235; Command: fastq_pair; Return code: 0; Memory used: 5.268GB
mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq
(6592)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 6592; Command: mv; Return code: 0; Memory used: 0.001GB
mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed.fastq
(6595)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 6595; Command: mv; Return code: 0; Memory used: 0.001GB
touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/repaired.flag
(6596)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 6596; 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_2/fastq/dups_repaired.flag
fastq_pair -t 102675166 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed_dups.fastq
(6597)Left paired: 26273211 Right paired: 26273211 Left single: 141535 Right single: 4488477 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_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_2/fastq/H9_treated_PRO-seq_2_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed_dups.fastq.single.fqCommand completed. Elapsed time: 0:02:34. Running peak memory: 6.557GB.
PID: 6597; Command: fastq_pair; Return code: 0; Memory used: 5.269GB
mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_trimmed.fastq
(7001)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 7001; Command: mv; Return code: 0; Memory used: 0.001GB
mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed_dups.fastq
(7003)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 7003; Command: mv; Return code: 0; Memory used: 0.001GB
touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/dups_repaired.flag
(7004)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 7004; Command: touch; Return code: 0; Memory used: 0.0GB
Prealignments (06-15 07:50:05) elapsed: 350.0 TIME
Prealignment assemblies: ['human_rDNA']
Map to human_rDNA (06-15 07:50:05) elapsed: 0.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/human_rDNA_bt2
mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/human_rDNA_bt2
(7005)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 7005; 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_2/prealignments/H9_treated_PRO-seq_2_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_2/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_R2.fq
(7006)
(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_2 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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' 28465823 reads; of these: 28465823 (100.00%) were unpaired; of these: 25736513 (90.41%) aligned 0 times 2729310 (9.59%) aligned exactly 1 time 0 (0.00%) aligned >1 times 9.59% overall alignment rate
Aligned_reads_human_rDNA
5458620.0 PEPPRO RES
Alignment_rate_human_rDNA
9.52 PEPPRO RES
Map to human_rDNA (06-15 07:54:07) elapsed: 242.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/human_rDNA_dups_bt2
mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/human_rDNA_dups_bt2
(7278)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 7278; Command: mkfifo; Return code: 0; Memory used: 0.002GB
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_2/prealignments/H9_treated_PRO-seq_2_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_2/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_dups_R2.fq
(7279)
(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_2 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/fastq/H9_treated_PRO-seq_2_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)
not gzipping output 2729310 reads skipped 0 reads lost File not added to cleanup: prealignments/human_rDNA_dups_bt2
Map to genome (06-15 07:57:59) elapsed: 231.0 TIME
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_fail_qc_dups.bam
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort.bam
bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_treated_PRO-seq_2 -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_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_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_2/aligned_hg38/tmpj5bu8aqe -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_temp.bam
(7724,7725,7726)2306063 reads skipped 0 reads lost 25736513 reads; of these: 25736513 (100.00%) were paired; of these: 10470203 (40.68%) aligned concordantly 0 times 12826144 (49.84%) aligned concordantly exactly 1 time 2440166 (9.48%) aligned concordantly >1 times ---- 10470203 pairs aligned concordantly 0 times; of these: 2441340 (23.32%) aligned discordantly 1 time ---- 8028863 pairs aligned 0 times concordantly or discordantly; of these: 16057726 mates make up the pairs; of these: 6731776 (41.92%) aligned 0 times 3441445 (21.43%) aligned exactly 1 time 5884505 (36.65%) aligned >1 times 86.92% overall alignment rate [bam_sort_core] merging from 15 files and 1 in-memory blocks...Command completed. Elapsed time: 0:49:01. Running peak memory: 6.557GB.
PID: 7724; Command: bowtie2; Return code: 0; Memory used: 3.778GB
PID: 7725; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 7726; Command: samtools; Return code: 0; Memory used: 0.906GB
samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort.bam
(13046)Command completed. Elapsed time: 0:01:33. Running peak memory: 6.557GB.
PID: 13046; 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_2/aligned_hg38/H9_treated_PRO-seq_2_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'
Mapped_reads
44741250 PEPPRO RES
QC_filtered_reads
25860518 PEPPRO RES
Aligned_reads
18880731.5 PEPPRO RES
Alignment_rate
32.92 PEPPRO RES
Total_efficiency
16.55 PEPPRO RES
Read_depth
3.37 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort_dups.bam
bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_treated_PRO-seq_2 -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_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_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_2/aligned_hg38/tmpj5bu8aqe -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_temp_dups.bam
(14640,14642,14643)23967148 reads; of these: 23967148 (100.00%) were paired; of these: 9441036 (39.39%) aligned concordantly 0 times 12234981 (51.05%) aligned concordantly exactly 1 time 2291131 (9.56%) aligned concordantly >1 times ---- 9441036 pairs aligned concordantly 0 times; of these: 2335210 (24.73%) aligned discordantly 1 time ---- 7105826 pairs aligned 0 times concordantly or discordantly; of these: 14211652 mates make up the pairs; of these: 6043583 (42.53%) aligned 0 times 3281410 (23.09%) aligned exactly 1 time 4886659 (34.38%) aligned >1 times 87.39% overall alignment rate [bam_sort_core] merging from 14 files and 1 in-memory blocks...Command completed. Elapsed time: 0:44:45. Running peak memory: 6.557GB.
PID: 14640; Command: bowtie2; Return code: 0; Memory used: 3.765GB
PID: 14642; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 14643; Command: samtools; Return code: 0; Memory used: 0.905GB
samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort_dups.bam
(19264)Command completed. Elapsed time: 0:01:23. Running peak memory: 6.557GB.
PID: 19264; Command: samtools; Return code: 0; Memory used: 0.018GB
Compress all unmapped read files (06-15 09:47:18) elapsed: 6560.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_R1.fq.gz
pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_R1.fq
(19418)Command completed. Elapsed time: 0:00:23. Running peak memory: 6.557GB.
PID: 19418; Command: pigz; Return code: 0; Memory used: 0.013GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_R2.fq.gz
pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/prealignments/H9_treated_PRO-seq_2_human_rDNA_unmap_R2.fq
(19451)Command completed. Elapsed time: 0:00:21. Running peak memory: 6.557GB.
PID: 19451; 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_2/aligned_hg38/H9_treated_PRO-seq_2_temp.bam.bai
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_temp.bam
(19488)Command completed. Elapsed time: 0:00:39. Running peak memory: 6.557GB.
PID: 19488; 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_2/aligned_hg38/H9_treated_PRO-seq_2_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3
Mitochondrial_reads
670904 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_noMT.bam
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort.bam
(19546)Command completed. Elapsed time: 0:00:32. Running peak memory: 6.557GB.
PID: 19546; 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_2/aligned_hg38/H9_treated_PRO-seq_2_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_2/aligned_hg38/chr_sizes.bed
(19574,19575,19576,19577)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 19575; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 19577; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 19574; Command: samtools; Return code: 0; Memory used: 0.011GB
PID: 19576; Command: awk; Return code: 0; Memory used: 0.0GB
samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_noMT.bam
(19579)Command completed. Elapsed time: 0:00:46. Running peak memory: 6.557GB.
PID: 19579; Command: samtools; Return code: 0; Memory used: 0.019GB
mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort.bam
(19690)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 19690; 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_2/aligned_hg38/H9_treated_PRO-seq_2_sort.bam
(19691)Command completed. Elapsed time: 0:00:28. Running peak memory: 6.557GB.
PID: 19691; Command: samtools; Return code: 0; Memory used: 0.011GB
Split BAM file (06-15 09:50:28) elapsed: 190.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE2.bam
samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam
(19978,19979)[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:02:51. Running peak memory: 6.557GB.
PID: 19978; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 19979; Command: samtools; Return code: 0; Memory used: 5.526GB
samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE2.bam
(20253,20254)[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:02:21. Running peak memory: 6.557GB.
PID: 20253; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 20254; Command: samtools; Return code: 0; Memory used: 4.484GB
Missing stat 'Maximum_read_length'
samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_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_2/aligned_hg38/H9_treated_PRO-seq_2_temp_dups.bam.bai
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_temp_dups.bam
(20756)Command completed. Elapsed time: 0:00:35. Running peak memory: 6.557GB.
PID: 20756; 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_2/aligned_hg38/H9_treated_PRO-seq_2_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_2/aligned_hg38/H9_treated_PRO-seq_2_sort_dups.bam
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort_dups.bam.bai Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_dups_PE1.bam
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_dups_PE2.bam
samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_dups_PE1.bam
(20791,20792)[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:02:46. Running peak memory: 6.557GB.
PID: 20791; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 20792; Command: samtools; Return code: 0; Memory used: 5.349GB
samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_dups_PE2.bam
(21036,21037)[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:02:11. Running peak memory: 6.557GB.
PID: 21036; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 21037; Command: samtools; Return code: 0; Memory used: 4.334GB
Calculate library complexity (06-15 10:02:11) elapsed: 703.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_preseq_out.txt
preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_dups_PE1.bam
(21548)BAM_INPUT TOTAL READS = 19595024 COUNTS_SUM = 19595024 DISTINCT READS = 1.48576e+07 DISTINCT COUNTS = 296 MAX COUNT = 22664 COUNTS OF 1 = 1.29529e+07 OBSERVED COUNTS (22665) 1 12952887 2 1171763 3 313507 4 140501 5 77968 6 49441 7 32956 8 23332 9 17067 10 12863 11 9993 12 8220 13 6438 14 5374 15 4272 16 3535 17 3085 18 2617 19 2187 20 1897 21 1621 22 1418 23 1206 24 1109 25 972 26 869 27 788 28 680 29 637 30 560 31 514 32 459 33 411 34 377 35 353 36 323 37 323 38 279 39 249 40 227 41 222 42 223 43 172 44 153 45 195 46 137 47 127 48 127 49 119 50 121 51 114 52 120 53 100 54 84 55 90 56 84 57 60 58 80 59 77 60 77 61 68 62 80 63 66 64 44 65 54 66 49 67 32 68 53 69 48 70 41 71 32 72 39 73 32 74 29 75 29 76 27 77 31 78 22 79 29 80 27 81 31 82 32 83 33 84 21 85 27 86 21 87 8 88 19 89 15 90 15 91 12 92 20 93 18 94 14 95 14 96 21 97 8 98 16 99 9 100 15 101 8 102 13 103 19 104 13 105 14 106 6 107 11 108 12 109 13 110 10 111 8 112 13 113 7 114 9 115 3 116 11 117 9 118 10 119 5 120 5 121 7 122 4 123 9 124 6 125 9 126 4 127 6 128 7 129 6 130 8 131 3 132 7 133 8 134 7 135 3 136 7 137 5 138 8 139 5 140 10 141 4 142 3 143 3 144 4 145 2 146 2 147 7 148 4 149 4 150 3 151 3 153 4 154 2 155 6 156 2 157 3 158 4 160 5 161 2 162 2 163 1 164 1 165 1 166 6 167 3 168 1 169 5 170 1 171 5 172 4 173 1 174 4 175 5 176 1 177 4 178 1 179 4 180 2 181 4 183 1 184 4 185 6 188 1 189 2 190 1 191 1 194 1 195 2 196 3 197 3 198 2 199 1 200 1 202 2 203 4 206 2 207 1 208 2 209 1 211 1 212 1 213 3 214 3 216 2 217 1 221 1 222 2 224 1 225 1 227 1 228 1 231 2 234 4 236 1 237 1 240 1 242 2 246 1 247 1 250 2 253 1 254 1 255 1 256 1 257 1 259 1 260 1 263 3 265 1 266 1 267 1 268 2 273 1 274 1 277 1 279 1 280 1 282 2 283 1 286 1 287 1 288 1 290 1 292 1 295 3 297 1 301 1 305 1 309 1 321 1 334 1 338 1 343 1 346 1 360 1 364 1 366 1 380 1 382 1 388 1 389 1 398 1 401 1 409 1 410 1 433 1 450 1 484 1 485 1 492 1 498 1 501 1 502 1 558 1 607 1 609 1 643 1 718 1 762 1 781 1 850 1 863 1 932 1 1085 1 1090 1 1227 1 1252 1 1420 1 1536 1 1567 1 1836 1 5591 1 5743 1 7315 1 15219 1 22664 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
Command completed. Elapsed time: 0:01:49. Running peak memory: 6.557GB.
PID: 21548; 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_2/QC_hg38/H9_treated_PRO-seq_2_preseq_yield.txt
preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_dups_PE1.bam
(21677)BAM_INPUT TOTAL READS = 19595024 DISTINCT READS = 1.48576e+07 DISTINCT COUNTS = 296 MAX COUNT = 22664 COUNTS OF 1 = 1.29529e+07 MAX TERMS = 100 OBSERVED COUNTS (22665) 1 12952887 2 1171763 3 313507 4 140501 5 77968 6 49441 7 32956 8 23332 9 17067 10 12863 11 9993 12 8220 13 6438 14 5374 15 4272 16 3535 17 3085 18 2617 19 2187 20 1897 21 1621 22 1418 23 1206 24 1109 25 972 26 869 27 788 28 680 29 637 30 560 31 514 32 459 33 411 34 377 35 353 36 323 37 323 38 279 39 249 40 227 41 222 42 223 43 172 44 153 45 195 46 137 47 127 48 127 49 119 50 121 51 114 52 120 53 100 54 84 55 90 56 84 57 60 58 80 59 77 60 77 61 68 62 80 63 66 64 44 65 54 66 49 67 32 68 53 69 48 70 41 71 32 72 39 73 32 74 29 75 29 76 27 77 31 78 22 79 29 80 27 81 31 82 32 83 33 84 21 85 27 86 21 87 8 88 19 89 15 90 15 91 12 92 20 93 18 94 14 95 14 96 21 97 8 98 16 99 9 100 15 101 8 102 13 103 19 104 13 105 14 106 6 107 11 108 12 109 13 110 10 111 8 112 13 113 7 114 9 115 3 116 11 117 9 118 10 119 5 120 5 121 7 122 4 123 9 124 6 125 9 126 4 127 6 128 7 129 6 130 8 131 3 132 7 133 8 134 7 135 3 136 7 137 5 138 8 139 5 140 10 141 4 142 3 143 3 144 4 145 2 146 2 147 7 148 4 149 4 150 3 151 3 153 4 154 2 155 6 156 2 157 3 158 4 160 5 161 2 162 2 163 1 164 1 165 1 166 6 167 3 168 1 169 5 170 1 171 5 172 4 173 1 174 4 175 5 176 1 177 4 178 1 179 4 180 2 181 4 183 1 184 4 185 6 188 1 189 2 190 1 191 1 194 1 195 2 196 3 197 3 198 2 199 1 200 1 202 2 203 4 206 2 207 1 208 2 209 1 211 1 212 1 213 3 214 3 216 2 217 1 221 1 222 2 224 1 225 1 227 1 228 1 231 2 234 4 236 1 237 1 240 1 242 2 246 1 247 1 250 2 253 1 254 1 255 1 256 1 257 1 259 1 260 1 263 3 265 1 266 1 267 1 268 2 273 1 274 1 277 1 279 1 280 1 282 2 283 1 286 1 287 1 288 1 290 1 292 1 295 3 297 1 301 1 305 1 309 1 321 1 334 1 338 1 343 1 346 1 360 1 364 1 366 1 380 1 382 1 388 1 389 1 398 1 401 1 409 1 410 1 433 1 450 1 484 1 485 1 492 1 498 1 501 1 502 1 558 1 607 1 609 1 643 1 718 1 762 1 781 1 850 1 863 1 932 1 1085 1 1090 1 1227 1 1252 1 1420 1 1536 1 1567 1 1836 1 5591 1 5743 1 7315 1 15219 1 22664 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
..........................................................................._.........................
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]
Command completed. Elapsed time: 0:01:53. Running peak memory: 6.557GB.
PID: 21677; 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_2/QC_hg38/H9_treated_PRO-seq_2_preseq_counts.txt
echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_preseq_counts.txt
(22125)Command completed. Elapsed time: 0:00:29. Running peak memory: 6.557GB.
PID: 22125; 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_2/QC_hg38/H9_treated_PRO-seq_2_preseq_plot.pdf
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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_2/QC_hg38/H9_treated_PRO-seq_2_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_preseq_plot
(22230)Processing H9_treated_PRO-seq_2 INFO: Found real counts for H9_treated_PRO-seq_2 - Total (M): 20.247016 Unique (M): 19.595024
Library complexity plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.557GB.
PID: 22230; Command: Rscript; Return code: 0; Memory used: 0.285GB
Library complexity
QC_hg38/H9_treated_PRO-seq_2_preseq_plot.pdf Library complexity QC_hg38/H9_treated_PRO-seq_2_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_2/QC_hg38/H9_treated_PRO-seq_2_preseq_yield.txt | awk '{print $2}'
Frac_exp_unique_at_10M
0.8189 PEPPRO RES
Calculate NRF, PBC1, and PBC2 (06-15 10:06:27) elapsed: 256.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam.bai
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam
(22265)Command completed. Elapsed time: 0:00:16. Running peak memory: 6.557GB.
PID: 22265; Command: samtools; Return code: 0; Memory used: 0.014GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_bamQC.tsv
(22287)Configured logger 'root' using pararead v0.6 Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam' Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/tmp_H9_treated_PRO-seq_2_PE1_0_3why97' Processing with 12 cores... Discarding 98 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr5_GL000208v1_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_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', '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_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270757v1'] 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_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270468v1', 'chrUn_KI270519v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270333v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270372v1', '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_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']Command completed. Elapsed time: 0:00:21. Running peak memory: 6.557GB.
PID: 22287; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.242GB
awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_bamQC.tsv
awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_bamQC.tsv
awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_bamQC.tsv
NRF
1.0 PEPPRO RES
PBC1
10123508.0 PEPPRO RES
PBC2
10123508.0 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_unmap.bam
samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_unmap.bam
(22340)Command completed. Elapsed time: 0:00:11. Running peak memory: 6.557GB.
PID: 22340; 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_2/aligned_hg38/H9_treated_PRO-seq_2_temp.bam
Unmapped_reads
6731776 PEPPRO RES
Split BAM by strand (06-15 10:07:22) elapsed: 55.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam
samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam
(22402)Command completed. Elapsed time: 0:01:08. Running peak memory: 6.557GB.
PID: 22402; 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_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam
(22482)Command completed. Elapsed time: 0:01:07. Running peak memory: 6.557GB.
PID: 22482; Command: samtools; Return code: 0; Memory used: 0.006GB
Calculate TSS enrichment (06-15 10:09:36) elapsed: 134.0 TIME
Missing stat 'TSS_non-coding_score'
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/plus_TSS.tsv
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/minus_TSS.tsv
sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed
(22655)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 22655; 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_2/QC_hg38/H9_treated_PRO-seq_2_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_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/H9_treated_PRO-seq_2_plus_TssEnrichment.txt
(22656)Command completed. Elapsed time: 0:00:07. Running peak memory: 6.557GB.
PID: 22656; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.884GB
TSS_coding_score
57.4 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/H9_treated_PRO-seq_2_minus_TssEnrichment.txt
(22689)Command completed. Elapsed time: 0:00:08. Running peak memory: 6.557GB.
PID: 22689; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.887GB
TSS_non-coding_score
16.5 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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_2/QC_hg38/H9_treated_PRO-seq_2_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_minus_TssEnrichment.txt
(22724)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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: 6.557GB.
PID: 22724; Command: Rscript; Return code: 0; Memory used: 0.316GB
TSS enrichment
QC_hg38/H9_treated_PRO-seq_2_TSSenrichment.pdf TSS enrichment QC_hg38/H9_treated_PRO-seq_2_TSSenrichment.png PEPPRO OBJ Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt
samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_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_2/QC_hg38/chr_order.txt
(22746,22747,22748,22749)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 22746; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 22748; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 22747; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 22749; 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_2/QC_hg38/chr_keep.txt
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_keep.txt
(22751)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 22751; Command: cut; Return code: 0; Memory used: 0.0GB
Calculate Pause Index (PI) (06-15 10:09:57) 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_2/QC_hg38/hg38_ensembl_tss.bed
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_ensembl_gene_body.bed
grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_ensembl_tss.bed
(22753,22754)Command completed. Elapsed time: 0:00:02. Running peak memory: 6.557GB.
PID: 22753; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 22754; Command: bedtools; Return code: 0; Memory used: 0.097GB
grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_ensembl_gene_body.bed
(22757,22758)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 22757; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 22758; 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_2/QC_hg38/H9_treated_PRO-seq_2_TSS_density.bed
bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/H9_treated_PRO-seq_2_TSS_density.bed
(22761,22762,22763,22764)Command completed. Elapsed time: 0:00:27. Running peak memory: 6.557GB.
PID: 22762; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 22764; Command: sort; Return code: 0; Memory used: 0.002GB
PID: 22761; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 22763; 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_2/QC_hg38/H9_treated_PRO-seq_2_gene_body_density.bed
bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_gene_body_density.bed
(23067,23068,23069)Command completed. Elapsed time: 0:00:31. Running peak memory: 6.557GB.
PID: 23068; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 23067; Command: bedtools; Return code: 0; Memory used: 0.058GB
PID: 23069; Command: sort; Return code: 0; Memory used: 0.003GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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_2/QC_hg38/H9_treated_PRO-seq_2_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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_2/QC_hg38/tmpf0akdhol
(23163,23164,23165)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 23163; Command: join; Return code: 0; Memory used: 0.001GB
PID: 23165; Command: env; Return code: 0; Memory used: 0.006GB
PID: 23164; 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_2/QC_hg38/tmpf0akdhol | 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_2/QC_hg38/H9_treated_PRO-seq_2_pause_index.bed
awk -v OFS=' ' '{ if ($5 > 0.0199168) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/tmpf0akdhol > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_pause_index.bed
(23172)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 23172; 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_2/QC_hg38/H9_treated_PRO-seq_2_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
59.52 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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_2/QC_hg38/H9_treated_PRO-seq_2_pause_index.bed
(23177)Pause index plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.557GB.
PID: 23177; Command: Rscript; Return code: 0; Memory used: 0.316GB
Pause index
QC_hg38/H9_treated_PRO-seq_2_pause_index.pdf Pause index QC_hg38/H9_treated_PRO-seq_2_pause_index.png PEPPRO OBJ Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_pause_index.bed.gz
pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_pause_index.bed
(23204)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 23204; Command: pigz; Return code: 0; Memory used: 0.002GB
Calculate Fraction of Reads in pre-mature mRNA (06-15 10:11:02) elapsed: 66.0 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_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam
18880731.5 7474169
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_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam
18880731.5 7075799
Minus_FRiP
0.37 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_gene_coverage.bed
grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_gene_sort.bed
(23276,23277)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 23276; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 23277; 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_2/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_gene_coverage.bed
(23279)Command completed. Elapsed time: 0:00:30. Running peak memory: 6.557GB.
PID: 23279; Command: bedtools; Return code: 0; Memory used: 0.061GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/raw/hg38_annotations.bed.gz
(23328)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 23328; 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_2/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/raw/hg38_annotations.bed
(23329)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 23329; Command: pigz; Return code: 0; Memory used: 0.002GB
Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 10:12:09) elapsed: 67.0 TIME
cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/raw/hg38_annotations.bed | sort -u
Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Enhancer
awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/raw/hg38_annotations.bed
(23338)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 23338; 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_2/QC_hg38/Enhancer_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Enhancer_sort.bed
(23340,23341,23342,23343)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 23340; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23341; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 23343; Command: bedtools; Return code: 0; Memory used: 0.012GB
PID: 23342; 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_2/QC_hg38/H9_treated_PRO-seq_2_Enhancer_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Enhancer_plus_coverage.bed
(23345)Command completed. Elapsed time: 0:00:13. Running peak memory: 6.557GB.
PID: 23345; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Enhancer_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Enhancer_minus_coverage.bed
(23359)Command completed. Elapsed time: 0:00:12. Running peak memory: 6.557GB.
PID: 23359; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter_sort.bed
(23405,23406,23407,23408)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 23405; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23406; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 23408; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 23407; 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_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_plus_coverage.bed
(23410)Command completed. Elapsed time: 0:00:14. Running peak memory: 6.557GB.
PID: 23410; Command: bedtools; Return code: 0; Memory used: 0.014GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_minus_coverage.bed
(23498)Command completed. Elapsed time: 0:00:14. Running peak memory: 6.557GB.
PID: 23498; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter Flanking Region
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter_Flanking_Region
mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter_Flanking_Region"
(23519)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 23519; 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_2/QC_hg38/Promoter_Flanking_Region_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter_Flanking_Region_sort.bed
(23520,23521,23522,23523)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 23520; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23522; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 23521; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 23523; 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_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_Flanking_Region_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_Flanking_Region_plus_coverage.bed
(23526)Command completed. Elapsed time: 0:00:13. Running peak memory: 6.557GB.
PID: 23526; 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_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_Flanking_Region_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_Flanking_Region_minus_coverage.bed
(23551)Command completed. Elapsed time: 0:00:13. Running peak memory: 6.557GB.
PID: 23551; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/5' UTR
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/5_UTR
mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/5_UTR"
(23590)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 23590; 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_2/QC_hg38/5_UTR_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/5_UTR_sort.bed
(23591,23592,23593,23594)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 23591; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23592; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 23594; Command: bedtools; Return code: 0; Memory used: 0.011GB
PID: 23593; 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_2/QC_hg38/H9_treated_PRO-seq_2_5_UTR_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_5_UTR_plus_coverage.bed
(23597)Command completed. Elapsed time: 0:00:13. Running peak memory: 6.557GB.
PID: 23597; 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_2/QC_hg38/H9_treated_PRO-seq_2_5_UTR_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_5_UTR_minus_coverage.bed
(23629)Command completed. Elapsed time: 0:00:13. Running peak memory: 6.557GB.
PID: 23629; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/3' UTR
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/3_UTR
mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/3_UTR"
(23650)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 23650; 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_2/QC_hg38/3_UTR_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/3_UTR_sort.bed
(23652,23653,23654,23655)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 23652; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23653; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 23655; Command: bedtools; Return code: 0; Memory used: 0.035GB
PID: 23654; 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_2/QC_hg38/H9_treated_PRO-seq_2_3_UTR_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_3_UTR_plus_coverage.bed
(23666)Command completed. Elapsed time: 0:00:13. Running peak memory: 6.557GB.
PID: 23666; 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_2/QC_hg38/H9_treated_PRO-seq_2_3_UTR_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_3_UTR_minus_coverage.bed
(23696)Command completed. Elapsed time: 0:00:13. Running peak memory: 6.557GB.
PID: 23696; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Exon
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Exon_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Exon_sort.bed
(23720,23721,23722,23723)Command completed. Elapsed time: 0:00:03. Running peak memory: 6.557GB.
PID: 23720; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23721; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 23723; Command: bedtools; Return code: 0; Memory used: 0.169GB
PID: 23722; 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_2/QC_hg38/H9_treated_PRO-seq_2_Exon_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Exon_plus_coverage.bed
(23736)Command completed. Elapsed time: 0:00:15. Running peak memory: 6.557GB.
PID: 23736; 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_2/QC_hg38/H9_treated_PRO-seq_2_Exon_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Exon_minus_coverage.bed
(23758)Command completed. Elapsed time: 0:00:14. Running peak memory: 6.557GB.
PID: 23758; Command: bedtools; Return code: 0; Memory used: 0.017GB
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Intron
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Intron_sort.bed
cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Intron_sort.bed
(23791,23792,23793,23794)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 23791; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 23793; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 23792; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 23794; Command: bedtools; Return code: 0; Memory used: 0.086GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Intron_plus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Intron_plus_coverage.bed
(23797)Command completed. Elapsed time: 0:00:16. Running peak memory: 6.557GB.
PID: 23797; Command: bedtools; Return code: 0; Memory used: 0.081GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Intron_minus_coverage.bed
bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Intron_minus_coverage.bed
(24580)Command completed. Elapsed time: 0:00:15. Running peak memory: 6.557GB.
PID: 24580; Command: bedtools; Return code: 0; Memory used: 0.039GB
Plot cFRiF/FRiF (06-15 10:15:29) elapsed: 200.0 TIME
samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam
Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_cFRiF.pdf
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_treated_PRO-seq_2 -z 3099922541 -n 10264898 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Intron_plus_coverage.bed
(24620)Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:37. Running peak memory: 6.557GB.
PID: 24620; Command: Rscript; Return code: 0; Memory used: 0.443GB
cFRiF
QC_hg38/H9_treated_PRO-seq_2_cFRiF.pdf cFRiF QC_hg38/H9_treated_PRO-seq_2_cFRiF.png PEPPRO OBJ Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_FRiF.pdf
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_treated_PRO-seq_2 -z 3099922541 -n 10264898 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_Intron_plus_coverage.bed
(24706)Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:27. Running peak memory: 6.557GB.
PID: 24706; Command: Rscript; Return code: 0; Memory used: 0.451GB
FRiF
QC_hg38/H9_treated_PRO-seq_2_FRiF.pdf FRiF QC_hg38/H9_treated_PRO-seq_2_FRiF.png PEPPRO OBJ
Calculate mRNA contamination (06-15 10:16:34) elapsed: 65.0 TIME
Missing stat 'mRNA_contamination'
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_exons_sort.bed
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_introns_sort.bed
grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/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_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_exons_sort.bed
(24751,24752)Command completed. Elapsed time: 0:00:05. Running peak memory: 6.557GB.
PID: 24752; Command: bedtools; Return code: 0; Memory used: 0.094GB
PID: 24751; 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_2/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_2/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_introns_sort.bed
(24776,24777,24779)Command completed. Elapsed time: 0:00:05. Running peak memory: 6.557GB.
PID: 24776; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 24779; Command: bedtools; Return code: 0; Memory used: 0.007GB
PID: 24777; 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_2/QC_hg38/H9_treated_PRO-seq_2_exons_coverage.bed
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_introns_coverage.bed
bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_exons_coverage.bed
(24789)Command completed. Elapsed time: 0:00:26. Running peak memory: 6.557GB.
PID: 24789; Command: bedtools; Return code: 0; Memory used: 0.01GB
bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_introns_coverage.bed
(24819)Command completed. Elapsed time: 0:00:28. Running peak memory: 6.557GB.
PID: 24819; Command: bedtools; Return code: 0; Memory used: 0.08GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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]/18.8807315)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_exons_rpkm.bed
(24855,24856,24857)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 24855; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 24857; Command: sort; Return code: 0; Memory used: 0.002GB
PID: 24856; 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_2/QC_hg38/H9_treated_PRO-seq_2_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]/18.8807315)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_introns_rpkm.bed
(24859,24860,24861)Command completed. Elapsed time: 0:00:01. Running peak memory: 6.557GB.
PID: 24859; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 24861; Command: sort; Return code: 0; Memory used: 0.003GB
PID: 24860; 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_2/QC_hg38/H9_treated_PRO-seq_2_exon_intron_ratios.bed
join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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_2/QC_hg38/H9_treated_PRO-seq_2_exon_intron_ratios.bed
(24864,24865,24866)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 24864; Command: join; Return code: 0; Memory used: 0.001GB
PID: 24866; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 24865; 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_2/QC_hg38/H9_treated_PRO-seq_2_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
1.16 PEPPRO RES Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_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_2/QC_hg38/H9_treated_PRO-seq_2_exon_intron_ratios.bed --annotate
(24872)mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.557GB.
PID: 24872; Command: Rscript; Return code: 0; Memory used: 0.302GB
mRNA contamination
QC_hg38/H9_treated_PRO-seq_2_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_treated_PRO-seq_2_mRNA_contamination.png PEPPRO OBJ Target to produce:/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_exon_intron_ratios.bed.gz
pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/QC_hg38/H9_treated_PRO-seq_2_exon_intron_ratios.bed
(24893)Command completed. Elapsed time: 0:00:00. Running peak memory: 6.557GB.
PID: 24893; Command: pigz; Return code: 0; Memory used: 0.003GB
Produce bigWig files (06-15 10:17:45) elapsed: 71.0 TIME
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_plus_exact_body_0-mer.bw
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_plus_smooth_body_0-mer.bw
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam
(24901)Command completed. Elapsed time: 0:00:08. Running peak memory: 6.557GB.
PID: 24901; 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_2/aligned_hg38/H9_treated_PRO-seq_2_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_2/signal_hg38/H9_treated_PRO-seq_2_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 18880731.5
(24908)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_2/aligned_hg38/H9_treated_PRO-seq_2_plus.bam' Temporary files will be stored in: 'tmp_H9_treated_PRO-seq_2_plus_cuttrace_yuuf674x' Processing with 4 cores... stdin is empty of data Discarding 111 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270720v1_random', 'chr14_KI270723v1_random', 'chr22_KI270735v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', '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_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_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1'] Keeping 84 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270468v1', 'chrUn_KI270519v1', 'chrUn_KI270589v1', 'chrUn_KI270372v1', '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_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 84 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_plus_exact_body_0-mer.bw' Merging 84 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_plus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:07:24. Running peak memory: 6.557GB.
PID: 24908; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.724GB
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_minus_exact_body_0-mer.bw
,/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_minus_smooth_body_0-mer.bw
samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam
(28151)Command completed. Elapsed time: 0:00:08. Running peak memory: 6.557GB.
PID: 28151; 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_2/aligned_hg38/H9_treated_PRO-seq_2_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_2/signal_hg38/H9_treated_PRO-seq_2_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 18880731.5
(28158)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_2/aligned_hg38/H9_treated_PRO-seq_2_minus.bam' Temporary files will be stored in: 'tmp_H9_treated_PRO-seq_2_minus_cuttrace_w7kmqi2c' Processing with 4 cores... Discarding 103 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr22_KI270736v1_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_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', '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_KI270757v1'] Keeping 92 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_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_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', '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_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 92 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_minus_exact_body_0-mer.bw' Merging 92 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_treated_PRO-seq_2/signal_hg38/H9_treated_PRO-seq_2_minus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:07:16. Running peak memory: 6.557GB.
PID: 28158; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.65GB
Pipeline completed. Epilogue
- Elapsed time (this run): 3:15:23
- Total elapsed time (all runs): 5:47:25
- Peak memory (this run): 6.5575 GB
- Pipeline completed time: 2020-06-15 10:32:41