### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_10 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 4 -M 8000 --input2 /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty`
* Compute host: udc-ba27-8
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/
* Pipeline started at: (06-11 17:53:46) elapsed: 0.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `4`
* `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_PRO-seq_10pct_PE1.fastq.gz']`
* `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz']`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `8000`
* `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`: `False`
* `sample_name`: `H9_PRO-seq_10`
* `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_PRO-seq_10pct_PE1.fastq.gz
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz
> `File_mb` 249.31 PEPPRO _RES_
> `Read_type` PAIRED PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-11 17:53:47) elapsed: 1.0 _TIME_
Number of input file sets: 2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz` (128153)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 128153; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz` (128544)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 128544; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_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_PRO-seq_10/fastq/H9_PRO-seq_10_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2.fastq`
> `pigz -f -p 4 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1.fastq` (129047)
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.002GB.
PID: 129047; Command: pigz; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 4 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2.fastq` (157719)
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.002GB.
PID: 157719; Command: pigz; Return code: 0; Memory used: 0.002GB
> `Raw_reads` 11560826 PEPPRO _RES_
> `Fastq_reads` 11560826 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz']
### FASTQ processing: (06-11 17:54:06) elapsed: 18.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq`
> `(cutadapt -j 4 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/cutadapt/H9_PRO-seq_10_R1_cutadapt.txt` (27602)
Command completed. Elapsed time: 0:00:23. Running peak memory: 0.442GB.
PID: 27602; Command: cutadapt; Return code: 0; Memory used: 0.442GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq` (27631,27633)
Command completed. Elapsed time: 0:00:07. Running peak memory: 0.442GB.
PID: 27631; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 27633; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 2830874 PEPPRO _RES_
> `Trim_loss_rate` 75.51 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq` (27649)
Started analysis of H9_PRO-seq_10_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 20% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 25% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_10_R1_processed.fastq
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Approx 40% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_10_R1_processed.fastq
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Approx 70% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_10_R1_processed.fastq
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Approx 95% complete for H9_PRO-seq_10_R1_processed.fastq
Analysis complete for H9_PRO-seq_10_R1_processed.fastq
Command completed. Elapsed time: 0:00:11. Running peak memory: 0.442GB.
PID: 27649; Command: fastqc; Return code: 0; Memory used: 0.159GB
> `FastQC report r1` fastqc/H9_PRO-seq_10_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_trimmed.fastq`
> `seqkit rmdup --threads 4 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_noadap.fastq` (27676)
[INFO][0m 81668 duplicated records removed
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.442GB.
PID: 27676; Command: seqkit; Return code: 0; Memory used: 0.266GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_trimmed.fastq` (32161,32206)
Command completed. Elapsed time: 0:00:04. Running peak memory: 0.442GB.
PID: 32161; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 32206; Command: seqtk; Return code: 0; Memory used: 0.002GB
> `grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/cutadapt/H9_PRO-seq_10_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 4579820.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/cutadapt/H9_PRO-seq_10_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_PRO-seq_10/cutadapt/H9_PRO-seq_10_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 2857948.0 PEPPRO _RES_
> `Duplicate_reads` 81668.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 49.4419 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/processed_R1.flag` (59403)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.442GB.
PID: 59403; 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_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq`
> `(cutadapt -j 4 -m 10 -O 1 -a GATCGTCGGACTGTAGAACTCTGAAC /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/cutadapt/H9_PRO-seq_10_R2_cutadapt.txt` (62872)
Command completed. Elapsed time: 0:00:17. Running peak memory: 0.442GB.
PID: 62872; Command: cutadapt; Return code: 0; Memory used: 0.418GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq` (172221,172300)
Command completed. Elapsed time: 0:00:04. Running peak memory: 0.442GB.
PID: 172221; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 172300; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 5661748 PEPPRO _RES_
> `Trim_loss_rate` 51.03 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq` (189973)
Started analysis of H9_PRO-seq_10_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_10_R1_processed.fastq
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Approx 40% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_10_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_10_R1_processed.fastq
Analysis complete for H9_PRO-seq_10_R1_processed.fastq
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.442GB.
PID: 189973; Command: fastqc; Return code: 0; Memory used: 0.16GB
> `FastQC report r1` fastqc/H9_PRO-seq_10_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_PRO-seq_10/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq` (33844)
Started analysis of H9_PRO-seq_10_R2_trimmed.fastq
Approx 5% complete for H9_PRO-seq_10_R2_trimmed.fastq
Approx 10% complete for H9_PRO-seq_10_R2_trimmed.fastq
Approx 15% complete for H9_PRO-seq_10_R2_trimmed.fastq
Approx 20% complete for H9_PRO-seq_10_R2_trimmed.fastq
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Approx 55% complete for H9_PRO-seq_10_R2_trimmed.fastq
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Approx 75% complete for H9_PRO-seq_10_R2_trimmed.fastq
Approx 80% complete for H9_PRO-seq_10_R2_trimmed.fastq
Approx 85% complete for H9_PRO-seq_10_R2_trimmed.fastq
Approx 90% complete for H9_PRO-seq_10_R2_trimmed.fastq
Approx 95% complete for H9_PRO-seq_10_R2_trimmed.fastq
Analysis complete for H9_PRO-seq_10_R2_trimmed.fastq
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.442GB.
PID: 33844; Command: fastqc; Return code: 0; Memory used: 0.156GB
> `FastQC report r2` fastqc/H9_PRO-seq_10_R2_trimmed_fastqc.html FastQC report r2 None PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/cutadapt/H9_PRO-seq_10.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/cutadapt/H9_PRO-seq_10.histogram`
> `fastq_pair -t 10404743 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_noadap.fastq` (33873)
Left paired: 2902040 Right paired: 2902040
Left single: 20425 Right single: 267392
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_noadap.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_noadap.fastq.single.fq
Command completed. Elapsed time: 0:00:22. Running peak memory: 0.455GB.
PID: 33873; Command: fastq_pair; Return code: 0; Memory used: 0.455GB
> `flash -q -t 4 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_noadap.fastq.paired.fq -o H9_PRO-seq_10 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/cutadapt` (33893)
Command completed. Elapsed time: 0:00:16. Running peak memory: 0.455GB.
PID: 33893; Command: flash; Return code: 0; Memory used: 0.07GB
### Plot adapter insertion distribution (06-11 17:56:21) elapsed: 135.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/cutadapt/H9_PRO-seq_10_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_PRO-seq_10/cutadapt/H9_PRO-seq_10.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/cutadapt -u 8` (66723)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:07. Running peak memory: 0.455GB.
PID: 66723; Command: Rscript; Return code: 0; Memory used: 0.204GB
> `Adapter insertion distribution` cutadapt/H9_PRO-seq_10_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_10_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_PRO-seq_10/cutadapt/H9_PRO-seq_10.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 (06-11 17:56:28) elapsed: 7.0 _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_PRO-seq_10/cutadapt/H9_PRO-seq_10.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_PRO-seq_10/cutadapt/H9_PRO-seq_10.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_PRO-seq_10/cutadapt/H9_PRO-seq_10.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_PRO-seq_10/cutadapt/H9_PRO-seq_10.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_PRO-seq_10/cutadapt/H9_PRO-seq_10.hist`
> `Degradation_ratio` 1.033 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed_dups.fastq`
> `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed_dups.fastq` (127018)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.455GB.
PID: 127018; Command: cp; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/processed_R2.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/processed_R2.flag` (139171)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.455GB.
PID: 139171; Command: touch; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/repaired.flag`
> `fastq_pair -t 10404743 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq` (140488)
Left paired: 2808336 Right paired: 2808336
Left single: 22538 Right single: 274561
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq.single.fq
Command completed. Elapsed time: 0:00:13. Running peak memory: 0.485GB.
PID: 140488; Command: fastq_pair; Return code: 0; Memory used: 0.485GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq` (37490)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.485GB.
PID: 37490; Command: mv; Return code: 0; Memory used: 0.001GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq` (38555)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.485GB.
PID: 38555; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/repaired.flag` (39270)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.485GB.
PID: 39270; Command: touch; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/dups_repaired.flag`
> `fastq_pair -t 10404743 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed_dups.fastq` (39903)
Left paired: 2734472 Right paired: 2734472
Left single: 18067 Right single: 348425
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed_dups.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed_dups.fastq.single.fq
Command completed. Elapsed time: 0:00:12. Running peak memory: 0.485GB.
PID: 39903; Command: fastq_pair; Return code: 0; Memory used: 0.478GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_trimmed.fastq` (136617)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.485GB.
PID: 136617; Command: mv; Return code: 0; Memory used: 0.001GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed_dups.fastq` (137486)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.485GB.
PID: 137486; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/dups_repaired.flag` (138385)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.485GB.
PID: 138385; Command: touch; Return code: 0; Memory used: 0.0GB
### Prealignments (06-11 17:56:56) elapsed: 28.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-11 17:56:56) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_bt2` (138973)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.485GB.
PID: 138973; 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_PRO-seq_10/prealignments/H9_PRO-seq_10_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_PRO-seq_10/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq` (139468)
> `(bowtie2 -p 4 -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_PRO-seq_10 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/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'
2808336 reads; of these:
2808336 (100.00%) were unpaired; of these:
2516719 (89.62%) aligned 0 times
291617 (10.38%) aligned exactly 1 time
0 (0.00%) aligned >1 times
10.38% overall alignment rate
> `Aligned_reads_human_rDNA` 583234.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 10.3 PEPPRO _RES_
### Map to human_rDNA (06-11 17:57:19) elapsed: 23.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_dups_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_dups_bt2` (146297)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.485GB.
PID: 146297; 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_PRO-seq_10/prealignments/H9_PRO-seq_10_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_PRO-seq_10/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_dups_R2.fq` (146865)
> `(bowtie2 -p 4 -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_PRO-seq_10 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)`
not gzipping output
291617 reads skipped
0 reads lost
File not added to cleanup: prealignments/human_rDNA_dups_bt2
### Map to genome (06-11 17:57:44) elapsed: 25.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_fail_qc_dups.bam
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam`
> `bowtie2 -p 4 --very-sensitive -X 2000 --rg-id H9_PRO-seq_10 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/tmpo1dzl55x -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp.bam` (170089,170091,170092)
268755 reads skipped
0 reads lost
2516719 reads; of these:
2516719 (100.00%) were paired; of these:
1043013 (41.44%) aligned concordantly 0 times
1209151 (48.04%) aligned concordantly exactly 1 time
264555 (10.51%) aligned concordantly >1 times
----
1043013 pairs aligned concordantly 0 times; of these:
231310 (22.18%) aligned discordantly 1 time
----
811703 pairs aligned 0 times concordantly or discordantly; of these:
1623406 mates make up the pairs; of these:
667337 (41.11%) aligned 0 times
349321 (21.52%) aligned exactly 1 time
606748 (37.38%) aligned >1 times
86.74% overall alignment rate
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:11:59. Running peak memory: 3.552GB.
PID: 170089; Command: bowtie2; Return code: 0; Memory used: 3.552GB
PID: 170092; Command: samtools; Return code: 0; Memory used: 0.894GB
PID: 170091; Command: samtools; Return code: 0; Memory used: 0.004GB
> `samtools view -q 10 -b -@ 4 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam` (171478)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.552GB.
PID: 171478; Command: samtools; Return code: 0; Memory used: 0.011GB
> `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_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 4366101 PEPPRO _RES_
> `QC_filtered_reads` 2551719 PEPPRO _RES_
> `Aligned_reads` 1814382.0 PEPPRO _RES_
> `Alignment_rate` 32.05 PEPPRO _RES_
> `Total_efficiency` 15.69 PEPPRO _RES_
> `Read_depth` 1.54 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort_dups.bam`
> `bowtie2 -p 4 --very-sensitive -X 2000 --rg-id H9_PRO-seq_10 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_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_PRO-seq_10/aligned_hg38/tmpo1dzl55x -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp_dups.bam` (172092,172093,172094)
2465717 reads; of these:
2465717 (100.00%) were paired; of these:
1005289 (40.77%) aligned concordantly 0 times
1199703 (48.66%) aligned concordantly exactly 1 time
260725 (10.57%) aligned concordantly >1 times
----
1005289 pairs aligned concordantly 0 times; of these:
229484 (22.83%) aligned discordantly 1 time
----
775805 pairs aligned 0 times concordantly or discordantly; of these:
1551610 mates make up the pairs; of these:
636007 (40.99%) aligned 0 times
345986 (22.30%) aligned exactly 1 time
569617 (36.71%) aligned >1 times
87.10% overall alignment rate
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:12:01. Running peak memory: 3.552GB.
PID: 172092; Command: bowtie2; Return code: 0; Memory used: 3.54GB
PID: 172094; Command: samtools; Return code: 0; Memory used: 0.894GB
PID: 172093; Command: samtools; Return code: 0; Memory used: 0.004GB
> `samtools view -q 10 -b -@ 4 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort_dups.bam` (173804)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.552GB.
PID: 173804; Command: samtools; Return code: 0; Memory used: 0.011GB
### Compress all unmapped read files (06-11 18:24:56) elapsed: 1632.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R1.fq.gz`
> `pigz -f -p 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R1.fq` (173839)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.552GB.
PID: 173839; Command: pigz; Return code: 0; Memory used: 0.003GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq.gz`
> `pigz -f -p 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq` (174058)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.552GB.
PID: 174058; Command: pigz; Return code: 0; Memory used: 0.004GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp.bam` (174076)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.552GB.
PID: 174076; Command: samtools; Return code: 0; Memory used: 0.017GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 83974 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam` (174093)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.552GB.
PID: 174093; Command: samtools; Return code: 0; Memory used: 0.006GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_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_PRO-seq_10/aligned_hg38/chr_sizes.bed` (174100,174101,174102,174103)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.552GB.
PID: 174101; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 174103; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 174100; Command: samtools; Return code: 0; Memory used: 0.008GB
PID: 174102; Command: awk; Return code: 0; Memory used: 0.0GB
> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/chr_sizes.bed -b -@ 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_noMT.bam` (174105)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.552GB.
PID: 174105; Command: samtools; Return code: 0; Memory used: 0.012GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam` (174125)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.552GB.
PID: 174125; Command: mv; Return code: 0; Memory used: 0.001GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam` (174126)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.552GB.
PID: 174126; Command: samtools; Return code: 0; Memory used: 0.006GB
### Split BAM file (06-11 18:25:26) elapsed: 30.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam | samtools sort - -@ 4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam` (174133,174134)
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
Command completed. Elapsed time: 0:00:18. Running peak memory: 3.552GB.
PID: 174133; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 174134; Command: samtools; Return code: 0; Memory used: 0.545GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam | samtools sort - -@ 4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE2.bam` (174188,174189)
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.552GB.
PID: 174188; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 174189; Command: samtools; Return code: 0; Memory used: 0.433GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_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_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp_dups.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp_dups.bam` (174253)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.552GB.
PID: 174253; Command: samtools; Return code: 0; Memory used: 0.018GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_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_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort_dups.bam`
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort_dups.bam.bai
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_dups_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort_dups.bam | samtools sort - -@ 4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_dups_PE1.bam` (174266,174267)
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
Command completed. Elapsed time: 0:00:18. Running peak memory: 3.552GB.
PID: 174266; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 174267; Command: samtools; Return code: 0; Memory used: 0.535GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort_dups.bam | samtools sort - -@ 4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_dups_PE2.bam` (174317,174318)
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.552GB.
PID: 174317; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 174318; Command: samtools; Return code: 0; Memory used: 0.461GB
### Calculate library complexity (06-11 18:26:46) elapsed: 80.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_out.txt`
> `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_dups_PE1.bam` (174366)
BAM_INPUT
TOTAL READS = 1966383
COUNTS_SUM = 1966383
DISTINCT READS = 1.84264e+06
DISTINCT COUNTS = 84
MAX COUNT = 4335
COUNTS OF 1 = 1.77576e+06
OBSERVED COUNTS (4336)
1 1775755
2 50849
3 8958
4 2905
5 1374
6 805
7 492
8 321
9 242
10 139
11 154
12 84
13 81
14 60
15 57
16 38
17 37
18 31
19 28
20 25
21 17
22 26
23 13
24 9
25 9
26 8
27 7
28 10
29 7
30 8
31 10
32 5
33 2
34 4
35 2
36 1
37 4
38 3
39 5
40 1
41 5
42 4
43 2
45 1
46 1
49 1
50 2
51 1
54 2
55 1
56 2
58 1
59 3
64 1
65 2
67 1
69 1
74 1
75 1
77 1
78 1
81 1
82 1
89 1
95 1
116 1
123 1
153 1
159 1
161 1
170 1
206 1
218 1
245 1
277 1
286 1
289 1
401 1
513 1
991 1
1224 1
1487 1
3220 1
4335 1
sample size: 1000000
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.552GB.
PID: 174366; Command: preseq; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_yield.txt`
> `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_dups_PE1.bam` (174388)
BAM_INPUT
TOTAL READS = 1966383
DISTINCT READS = 1.84264e+06
DISTINCT COUNTS = 84
MAX COUNT = 4335
COUNTS OF 1 = 1.77576e+06
MAX TERMS = 42
OBSERVED COUNTS (4336)
1 1775755
2 50849
3 8958
4 2905
5 1374
6 805
7 492
8 321
9 242
10 139
11 154
12 84
13 81
14 60
15 57
16 38
17 37
18 31
19 28
20 25
21 17
22 26
23 13
24 9
25 9
26 8
27 7
28 10
29 7
30 8
31 10
32 5
33 2
34 4
35 2
36 1
37 4
38 3
39 5
40 1
41 5
42 4
43 2
45 1
46 1
49 1
50 2
51 1
54 2
55 1
56 2
58 1
59 3
64 1
65 2
67 1
69 1
74 1
75 1
77 1
78 1
81 1
82 1
89 1
95 1
116 1
123 1
153 1
159 1
161 1
170 1
206 1
218 1
245 1
277 1
286 1
289 1
401 1
513 1
991 1
1224 1
1487 1
3220 1
4335 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
.................................................._..............................._...................
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]
Command completed. Elapsed time: 0:00:13. Running peak memory: 3.552GB.
PID: 174388; Command: preseq; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_counts.txt`
> `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_counts.txt` (174413)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.552GB.
PID: 174413; Command: echo; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_plot` (174425)
Processing H9_PRO-seq_10
INFO: Found real counts for H9_PRO-seq_10 - Total (M): 1.945718 Unique (M): 1.966383
Library complexity plot completed!
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.552GB.
PID: 174425; Command: Rscript; Return code: 0; Memory used: 0.185GB
> `Library complexity` QC_hg38/H9_PRO-seq_10_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/H9_PRO-seq_10_preseq_yield.txt | awk '{print $2}'`
> `Frac_exp_unique_at_10M` 0.8545 PEPPRO _RES_
### Calculate NRF, PBC1, and PBC2 (06-11 18:27:22) elapsed: 36.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam` (174454)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.552GB.
PID: 174454; Command: samtools; Return code: 0; Memory used: 0.008GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_bamQC.tsv`
> `/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam -c 4 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_bamQC.tsv` (174458)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/tmp_H9_PRO-seq_10_PE1_o9vn6o75'
Processing with 4 cores...
Discarding 128 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr14_KI270722v1_random', 'chr14_KI270723v1_random', 'chr14_KI270725v1_random', 'chr17_KI270729v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000224v1', 'chrUn_GL000226v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1']
Keeping 67 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_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270730v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.552GB.
PID: 174458; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 0.36GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_bamQC.tsv`
> `NRF` 1.0 PEPPRO _RES_
> `PBC1` 972859.0 PEPPRO _RES_
> `PBC2` 972859.0 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_unmap.bam`
> `samtools view -b -@ 4 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_unmap.bam` (174485)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.552GB.
PID: 174485; Command: samtools; Return code: 0; Memory used: 0.006GB
> `samtools view -c -f 4 -@ 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_temp.bam`
> `Unmapped_reads` 667337 PEPPRO _RES_
### Split BAM by strand (06-11 18:27:34) elapsed: 12.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam` (174507)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.552GB.
PID: 174507; 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_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam` (174522)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.552GB.
PID: 174522; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-11 18:27:49) elapsed: 15.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (174539)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.552GB.
PID: 174539; Command: sed; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_plus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/plus_TSS.tsv -p ends -c 4 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_plus_TssEnrichment.txt` (174541)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.552GB.
PID: 174541; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.224GB
> `TSS_coding_score` 33.6 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_minus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/minus_TSS.tsv -p ends -c 4 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_minus_TssEnrichment.txt` (174558)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.552GB.
PID: 174558; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.227GB
> `TSS_non-coding_score` 12.2 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSSenrichment.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_minus_TssEnrichment.txt` (174580)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_minus_TssEnrichment.txt
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
TSS enrichment plot completed!
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.552GB.
PID: 174580; Command: Rscript; Return code: 0; Memory used: 0.275GB
> `TSS enrichment` QC_hg38/H9_PRO-seq_10_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_10_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/chr_order.txt` (174619,174620,174621,174622)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.552GB.
PID: 174619; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 174621; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 174620; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 174622; Command: awk; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_keep.txt` (174624)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.552GB.
PID: 174624; Command: cut; Return code: 0; Memory used: 0.002GB
### Calculate Pause Index (PI) (06-11 18:28:04) elapsed: 15.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/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_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_tss.bed` (174626,174627)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.552GB.
PID: 174626; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 174627; Command: bedtools; Return code: 0; Memory used: 0.093GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/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_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_gene_body.bed` (174635,174636)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.552GB.
PID: 174635; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 174636; Command: bedtools; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/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_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSS_density.bed` (174638,174639,174640,174641)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.552GB.
PID: 174638; Command: bedtools; Return code: 0; Memory used: 0.005GB
PID: 174640; Command: sort; Return code: 0; Memory used: 0.007GB
PID: 174639; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 174641; Command: sort; Return code: 0; Memory used: 0.009GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_gene_body_density.bed` (174652,174653,174654)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.552GB.
PID: 174652; Command: bedtools; Return code: 0; Memory used: 0.03GB
PID: 174654; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 174653; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_pause_index.bed`
awk: cmd. line:1: { if ($5 == ){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}
awk: cmd. line:1: ^ syntax error
awk: cmd. line:1: { if ($5 == ){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}
awk: cmd. line:1: ^ syntax error
> `join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/tmpqe2mrkhv` (174664,174665,174666)
Got SIGTERM. Failing gracefully... (06-11 18:55:15) elapsed: 1631.0 _TIME_
Child process 139468 (perl) was already terminated.
Child process 146865 (perl) was already terminated.
Child process 174664 (join) terminated after 0 sec.
Setting dynamic recover file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/recover.lock.QC_hg38__H9_PRO-seq_10_pause_index.bed
### Pipeline failed at: (06-11 18:55:15) elapsed: 0.0 _TIME_
Total time: 1:01:29
Failure reason: SIGTERM
Pipeline aborted.
### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_10 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 4 -M 8000 --input2 /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba25-32c0
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/
* Pipeline started at: (06-11 19:13:06) elapsed: 0.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `4`
* `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_PRO-seq_10pct_PE1.fastq.gz']`
* `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz']`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `8000`
* `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_PRO-seq_10`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `PAIRED`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `8`
* `verbosity`: `None`
----------------------------------------
Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE1.fastq.gz
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz
> `File_mb` 249.31 PEPPRO _RES_
> `Read_type` PAIRED PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-11 19:13:07) elapsed: 1.0 _TIME_
Number of input file sets: 2
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz'
Found .fastq.gz file
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1.fastq`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz']
### FASTQ processing: (06-11 19:13:07) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/processed_R1.flag`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/processed_R2.flag`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/repaired.flag`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/dups_repaired.flag`
### Prealignments (06-11 19:13:07) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-11 19:13:07) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_bt2` (83103)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.002GB.
PID: 83103; Command: mkfifo; Return code: 0; Memory used: 0.002GB
File not added to cleanup: prealignments/human_rDNA_bt2
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq.gz`
File not added to cleanup: prealignments/human_rDNA_bt2
### Map to human_rDNA (06-11 19:13:07) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_dups_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_dups_bt2` (83104)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.002GB.
PID: 83104; Command: mkfifo; Return code: 0; Memory used: 0.0GB
File not added to cleanup: prealignments/human_rDNA_dups_bt2
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq.gz`
File not added to cleanup: prealignments/human_rDNA_dups_bt2
### Map to genome (06-11 19:13:07) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam`
### Compress all unmapped read files (06-11 19:13:07) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R1.fq.gz`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq.gz`
### Split BAM file (06-11 19:13:07) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE2.bam`
### Calculate NRF, PBC1, and PBC2 (06-11 19:13:07) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam.bai`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_bamQC.tsv`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_unmap.bam`
### Split BAM by strand (06-11 19:13:07) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam`
### Calculate TSS enrichment (06-11 19:13:07) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSSenrichment.pdf`
> `TSS enrichment` QC_hg38/H9_PRO-seq_10_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_10_TSSenrichment.png PEPPRO _OBJ_
### Calculate Pause Index (PI) (06-11 19:13:07) elapsed: 0.0 _TIME_
Missing stat 'Pause_index'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_tss.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_gene_body.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSS_density.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_gene_body_density.bed`
Found lock file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/lock.QC_hg38__H9_PRO-seq_10_pause_index.bed
Overwriting target...
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/tmp5czd4m_l` (83111,83112,83114)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.004GB.
PID: 83111; Command: join; Return code: 0; Memory used: 0.001GB
PID: 83114; Command: env; Return code: 0; Memory used: 0.004GB
PID: 83112; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/tmp5czd4m_l | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}`
/bin/sh: -c: line 0: unexpected EOF while looking for matching `''
/bin/sh: -c: line 1: syntax error: unexpected end of file
### Pipeline failed at: (06-11 19:13:08) elapsed: 0.0 _TIME_
Total time: 0:00:02
Failure reason: Command 'awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/tmp5czd4m_l | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}' returned non-zero exit status 1.
### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_10 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 4 -M 8000 --input2 /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-aj37-17c1
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/
* Pipeline started at: (06-14 21:18:39) elapsed: 5.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16373 insertions(+), 3522 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `4`
* `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_PRO-seq_10pct_PE1.fastq.gz']`
* `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz']`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `8000`
* `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_PRO-seq_10`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `PAIRED`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `8`
* `verbosity`: `None`
----------------------------------------
Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE1.fastq.gz
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_10pct_PE2.fastq.gz
> `File_mb` 249.31 PEPPRO _RES_
> `Read_type` PAIRED PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-14 21:18:40) elapsed: 1.0 _TIME_
Number of input file sets: 2
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz'
Found .fastq.gz file
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R1.fastq`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/H9_PRO-seq_10_R2.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/H9_PRO-seq_10_R2.fastq.gz']
### FASTQ processing: (06-14 21:18:40) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/processed_R1.flag`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/processed_R2.flag`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/repaired.flag`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/fastq/dups_repaired.flag`
### Prealignments (06-14 21:18:40) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-14 21:18:40) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_bt2` (315116)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 315116; Command: mkfifo; Return code: 0; Memory used: 0.0GB
File not added to cleanup: prealignments/human_rDNA_bt2
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq.gz`
File not added to cleanup: prealignments/human_rDNA_bt2
### Map to human_rDNA (06-14 21:18:40) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_dups_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/human_rDNA_dups_bt2` (315213)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 315213; Command: mkfifo; Return code: 0; Memory used: 0.0GB
File not added to cleanup: prealignments/human_rDNA_dups_bt2
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq.gz`
File not added to cleanup: prealignments/human_rDNA_dups_bt2
### Map to genome (06-14 21:18:40) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_sort.bam`
### Compress all unmapped read files (06-14 21:18:40) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R1.fq.gz`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/prealignments/H9_PRO-seq_10_human_rDNA_unmap_R2.fq.gz`
### Split BAM file (06-14 21:18:40) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE2.bam`
### Calculate NRF, PBC1, and PBC2 (06-14 21:18:40) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam.bai`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_bamQC.tsv`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_unmap.bam`
### Split BAM by strand (06-14 21:18:40) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam`
### Calculate TSS enrichment (06-14 21:18:40) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSSenrichment.pdf`
> `TSS enrichment` QC_hg38/H9_PRO-seq_10_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_10_TSSenrichment.png PEPPRO _OBJ_
### Calculate Pause Index (PI) (06-14 21:18:40) elapsed: 0.0 _TIME_
Missing stat 'Pause_index'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_tss.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_ensembl_gene_body.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSS_density.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_gene_body_density.bed`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/H9_PRO-seq_10_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/tmplttv258v` (315424,315431,315443)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.004GB.
PID: 315424; Command: join; Return code: 0; Memory used: 0.001GB
PID: 315443; Command: env; Return code: 0; Memory used: 0.004GB
PID: 315431; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/tmplttv258v | 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_PRO-seq_10/QC_hg38/H9_PRO-seq_10_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.00261755) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/tmplttv258v > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_pause_index.bed` (316092)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.004GB.
PID: 316092; Command: awk; Return code: 0; Memory used: 0.002GB
> `sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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` 33.58 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/H9_PRO-seq_10_pause_index.bed` (316301)
Pause index plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.204GB.
PID: 316301; Command: Rscript; Return code: 0; Memory used: 0.204GB
> `Pause index` QC_hg38/H9_PRO-seq_10_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_10_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_pause_index.bed.gz`
> `pigz -f -p 4 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_pause_index.bed` (325373)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.204GB.
PID: 325373; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-14 21:18:47) elapsed: 7.0 _TIME_
Missing stat 'Plus_FRiP'
> `samtools view -@ 4 -c -L /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam`
1814382.0 704966
> `Plus_FRiP` 0.39 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_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam`
1814382.0 655479
> `Minus_FRiP` 0.36 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/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_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_gene_sort.bed` (329280,329284)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.204GB.
PID: 329280; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 329284; Command: bedtools; Return code: 0; Memory used: 0.005GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_gene_coverage.bed` (329856)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.204GB.
PID: 329856; Command: bedtools; Return code: 0; Memory used: 0.031GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/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_PRO-seq_10/raw/hg38_annotations.bed.gz` (331694)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.204GB.
PID: 331694; Command: ln; Return code: 0; Memory used: 0.0GB
> `pigz -f -p 4 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/hg38_annotations.bed` (331697)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.204GB.
PID: 331697; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-14 21:18:58) elapsed: 10.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/raw/hg38_annotations.bed` (331714)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.204GB.
PID: 331714; Command: awk; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Enhancer_sort.bed` (331762,331763,331764,331765)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.204GB.
PID: 331762; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 331763; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 331765; Command: bedtools; Return code: 0; Memory used: 0.044GB
PID: 331764; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Enhancer_plus_coverage.bed` (331783)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331783; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Enhancer_minus_coverage.bed` (331788)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331788; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_sort.bed` (331801,331802,331803,331804)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.204GB.
PID: 331801; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 331802; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 331804; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 331803; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_plus_coverage.bed` (331807)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331807; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_minus_coverage.bed` (331816)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331816; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_Flanking_Region"` (331821)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.204GB.
PID: 331821; Command: mv; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/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_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_Flanking_Region_sort.bed` (331822,331823,331824,331825)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.204GB.
PID: 331822; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 331824; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 331823; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 331825; Command: bedtools; Return code: 0; Memory used: 0.048GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_Flanking_Region_plus_coverage.bed` (331828)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331828; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_Flanking_Region_minus_coverage.bed` (331843)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331843; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/5_UTR"` (331853)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.204GB.
PID: 331853; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/5_UTR_sort.bed` (331854,331855,331856,331857)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.204GB.
PID: 331854; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 331855; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 331857; Command: bedtools; Return code: 0; Memory used: 0.012GB
PID: 331856; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_5_UTR_plus_coverage.bed` (331860)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331860; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_5_UTR_minus_coverage.bed` (331863)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331863; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/3_UTR"` (331868)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.204GB.
PID: 331868; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/3_UTR_sort.bed` (331869,331870,331871,331872)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.204GB.
PID: 331869; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 331870; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 331872; Command: bedtools; Return code: 0; Memory used: 0.011GB
PID: 331871; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_3_UTR_plus_coverage.bed` (331875)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331875; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_3_UTR_minus_coverage.bed` (331884)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331884; Command: bedtools; Return code: 0; Memory used: 0.007GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Exon_sort.bed` (331889,331890,331891,331892)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.204GB.
PID: 331889; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 331890; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 331892; Command: bedtools; Return code: 0; Memory used: 0.158GB
PID: 331891; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Exon_plus_coverage.bed` (331899)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.204GB.
PID: 331899; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Exon_minus_coverage.bed` (331910)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331910; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Intron_sort.bed` (331918,331919,331920,331921)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.204GB.
PID: 331918; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 331920; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 331919; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 331921; Command: bedtools; Return code: 0; Memory used: 0.011GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Intron_plus_coverage.bed` (331927)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.204GB.
PID: 331927; Command: bedtools; Return code: 0; Memory used: 0.013GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Intron_minus_coverage.bed` (331945)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.204GB.
PID: 331945; Command: bedtools; Return code: 0; Memory used: 0.014GB
### Plot cFRiF/FRiF (06-14 21:19:36) elapsed: 38.0 _TIME_
> `samtools view -@ 4 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_10 -z 3099922541 -n 994670 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Intron_plus_coverage.bed` (331959)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:35. Running peak memory: 0.44GB.
PID: 331959; Command: Rscript; Return code: 0; Memory used: 0.44GB
> `cFRiF` QC_hg38/H9_PRO-seq_10_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_10_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_10 -z 3099922541 -n 994670 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_Intron_plus_coverage.bed` (332292)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:29. Running peak memory: 0.44GB.
PID: 332292; Command: Rscript; Return code: 0; Memory used: 0.44GB
> `FRiF` QC_hg38/H9_PRO-seq_10_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_10_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-14 21:20:41) elapsed: 65.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/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_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_exons_sort.bed` (332350,332351)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.44GB.
PID: 332351; Command: bedtools; Return code: 0; Memory used: 0.08GB
PID: 332350; Command: grep; Return code: 0; Memory used: 0.004GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/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_PRO-seq_10/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_introns_sort.bed` (332358,332359,332360)
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.44GB.
PID: 332358; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 332360; Command: bedtools; Return code: 0; Memory used: 0.004GB
PID: 332359; Command: bedtools; Return code: 0; Memory used: 0.033GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_exons_coverage.bed` (332366)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.44GB.
PID: 332366; Command: bedtools; Return code: 0; Memory used: 0.007GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_introns_coverage.bed` (332371)
Command completed. Elapsed time: 0:00:04. Running peak memory: 0.44GB.
PID: 332371; Command: bedtools; Return code: 0; Memory used: 0.014GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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]/1.814382)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_exons_rpkm.bed` (332376,332377,332378)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.44GB.
PID: 332376; Command: awk; Return code: 0; Memory used: 0.009GB
PID: 332378; Command: sort; Return code: 0; Memory used: 0.002GB
PID: 332377; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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]/1.814382)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_introns_rpkm.bed` (332380,332381,332382)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.44GB.
PID: 332380; Command: awk; Return code: 0; Memory used: 0.009GB
PID: 332382; Command: sort; Return code: 0; Memory used: 0.003GB
PID: 332381; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/H9_PRO-seq_10_exon_intron_ratios.bed` (332385,332386,332387)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.44GB.
PID: 332385; Command: join; Return code: 0; Memory used: 0.001GB
PID: 332387; Command: sort; Return code: 0; Memory used: 0.003GB
PID: 332386; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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` 1.34 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_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_PRO-seq_10/QC_hg38/H9_PRO-seq_10_exon_intron_ratios.bed --annotate` (332393)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.44GB.
PID: 332393; Command: Rscript; Return code: 0; Memory used: 0.263GB
> `mRNA contamination` QC_hg38/H9_PRO-seq_10_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_10_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_exon_intron_ratios.bed.gz`
> `pigz -f -p 4 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/QC_hg38/H9_PRO-seq_10_exon_intron_ratios.bed` (332414)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.44GB.
PID: 332414; Command: pigz; Return code: 0; Memory used: 0.002GB
### Produce bigWig files (06-14 21:21:06) elapsed: 25.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam` (332421)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.44GB.
PID: 332421; 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_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_plus_smooth_body_0-mer.bw -p 2 --variable-step --tail-edge --scale 1814382.0` (332424)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_plus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_10_plus_cuttrace_j1my62qp'
Processing with 1 cores...
Discarding 141 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr1_KI270714v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr15_KI270727v1_random', 'chr17_KI270729v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_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_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000224v1', 'chrUn_GL000226v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000218v1']
Keeping 54 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_KI270711v1_random', 'chr1_KI270713v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270726v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270730v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270747v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrEBV']
Reduce step (merge files)...
Merging 54 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_plus_exact_body_0-mer.bw'
Merging 54 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:17:20. Running peak memory: 1.85GB.
PID: 332424; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 1.85GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam` (135565)
Command completed. Elapsed time: 0:00:01. Running peak memory: 1.85GB.
PID: 135565; Command: samtools; Return code: 0; Memory used: 0.01GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_minus_smooth_body_0-mer.bw -p 2 --variable-step --tail-edge --scale 1814382.0` (135567)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/aligned_hg38/H9_PRO-seq_10_minus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_10_minus_cuttrace_28dlyiwy'
Processing with 1 cores...
stdin is empty of data
Discarding 141 chunk(s) of reads: ['chrM', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_KI270723v1_random', 'chr14_KI270725v1_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', '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_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1']
Keeping 54 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr9_KI270718v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_KI270743v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270750v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 54 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_minus_exact_body_0-mer.bw'
Merging 54 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_10/signal_hg38/H9_PRO-seq_10_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:17:01. Running peak memory: 2.477GB.
PID: 135567; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.477GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:36:56
* Total elapsed time (all runs): 3:48:32
* Peak memory (this run): 2.4766 GB
* Pipeline completed time: 2020-06-14 21:55:30