### 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
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Approx 45% complete for H9_treated_PRO-seq_2_R1_processed.fastq
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Approx 55% complete for H9_treated_PRO-seq_2_R1_processed.fastq
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Analysis complete for H9_treated_PRO-seq_2_R1_processed.fastq
Command 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 removed
Command 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
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Analysis complete for H9_treated_PRO-seq_2_R1_processed.fastq
Command 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
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Analysis complete for H9_treated_PRO-seq_2_R2_trimmed.fastq
Command 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.fq
Command 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.fq
Command 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.fq
Command 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