### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_60 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_60pct_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --input2 /project/shefflab/data//guertin/fastq/H9_PRO-seq_60pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba27-33c1
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/
* Pipeline started at: (06-15 07:17:18) elapsed: 1.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_60pct_PE1.fastq.gz']`
* `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_60pct_PE2.fastq.gz']`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `12000`
* `new_start`: `False`
* `no_fifo`: `False`
* `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline`
* `paired_end`: `True`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `PRO`
* `recover`: `True`
* `sample_name`: `H9_PRO-seq_60`
* `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_60pct_PE1.fastq.gz
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_60pct_PE2.fastq.gz
> `File_mb` 1443.18 PEPPRO _RES_
> `Read_type` PAIRED PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-15 07:17:20) 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_60/raw/H9_PRO-seq_60_R1.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_60pct_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/H9_PRO-seq_60_R1.fastq.gz` (420360)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 420360; 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_60/raw/H9_PRO-seq_60_R1.fastq.gz'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/H9_PRO-seq_60_R2.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_60pct_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/H9_PRO-seq_60_R2.fastq.gz` (420363)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 420363; 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_60/raw/H9_PRO-seq_60_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_60/fastq/H9_PRO-seq_60_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2.fastq`
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/H9_PRO-seq_60_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1.fastq` (420365)
Command completed. Elapsed time: 0:02:03. Running peak memory: 0.002GB.
PID: 420365; Command: pigz; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/H9_PRO-seq_60_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2.fastq` (420489)
Command completed. Elapsed time: 0:01:31. Running peak memory: 0.002GB.
PID: 420489; Command: pigz; Return code: 0; Memory used: 0.002GB
> `Raw_reads` 69434420 PEPPRO _RES_
> `Fastq_reads` 69434420 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/H9_PRO-seq_60_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/H9_PRO-seq_60_R2.fastq.gz']
### FASTQ processing: (06-15 07:22:05) elapsed: 286.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq`
> `(cutadapt -j 12 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/cutadapt/H9_PRO-seq_60_R1_cutadapt.txt` (420986)
Command completed. Elapsed time: 0:00:55. Running peak memory: 3.008GB.
PID: 420986; Command: cutadapt; Return code: 0; Memory used: 3.008GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq` (421131,421132)
Command completed. Elapsed time: 0:00:41. Running peak memory: 3.008GB.
PID: 421131; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 421132; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 16997812 PEPPRO _RES_
> `Trim_loss_rate` 75.52 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq` (421189)
Started analysis of H9_PRO-seq_60_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 20% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 25% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 35% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_60_R1_processed.fastq
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Approx 70% complete for H9_PRO-seq_60_R1_processed.fastq
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Approx 95% complete for H9_PRO-seq_60_R1_processed.fastq
Analysis complete for H9_PRO-seq_60_R1_processed.fastq
Command completed. Elapsed time: 0:00:38. Running peak memory: 3.008GB.
PID: 421189; Command: fastqc; Return code: 0; Memory used: 0.168GB
> `FastQC report r1` fastqc/H9_PRO-seq_60_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_60/fastq/H9_PRO-seq_60_R1_trimmed.fastq`
> `seqkit rmdup --threads 12 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_noadap.fastq` (421287)
[INFO][0m 1324320 duplicated records removed
Command completed. Elapsed time: 0:00:32. Running peak memory: 3.008GB.
PID: 421287; Command: seqkit; Return code: 0; Memory used: 1.036GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_trimmed.fastq` (421345,421346)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.008GB.
PID: 421345; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 421346; 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_60/cutadapt/H9_PRO-seq_60_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 27510738.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/cutadapt/H9_PRO-seq_60_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_60/cutadapt/H9_PRO-seq_60_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 17169444.0 PEPPRO _RES_
> `Duplicate_reads` 1324320.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 49.4551 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/processed_R1.flag` (421625)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.008GB.
PID: 421625; 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_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq`
> `(cutadapt -j 12 -m 10 -O 1 -a GATCGTCGGACTGTAGAACTCTGAAC /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/cutadapt/H9_PRO-seq_60_R2_cutadapt.txt` (421627)
Command completed. Elapsed time: 0:00:47. Running peak memory: 3.008GB.
PID: 421627; Command: cutadapt; Return code: 0; Memory used: 2.318GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq` (421709,421710)
Command completed. Elapsed time: 0:00:21. Running peak memory: 3.008GB.
PID: 421709; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 421710; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 33995624 PEPPRO _RES_
> `Trim_loss_rate` 51.04 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq` (421745)
Started analysis of H9_PRO-seq_60_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_60_R1_processed.fastq
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Approx 35% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_60_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_60_R1_processed.fastq
Analysis complete for H9_PRO-seq_60_R1_processed.fastq
Command completed. Elapsed time: 0:00:37. Running peak memory: 3.008GB.
PID: 421745; Command: fastqc; Return code: 0; Memory used: 0.166GB
> `FastQC report r1` fastqc/H9_PRO-seq_60_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_60/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq` (421815)
Started analysis of H9_PRO-seq_60_R2_trimmed.fastq
Approx 5% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 10% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 15% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 20% complete for H9_PRO-seq_60_R2_trimmed.fastq
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Approx 40% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 45% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 50% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 55% complete for H9_PRO-seq_60_R2_trimmed.fastq
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Approx 75% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 80% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 85% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 90% complete for H9_PRO-seq_60_R2_trimmed.fastq
Approx 95% complete for H9_PRO-seq_60_R2_trimmed.fastq
Analysis complete for H9_PRO-seq_60_R2_trimmed.fastq
Command completed. Elapsed time: 0:00:33. Running peak memory: 3.008GB.
PID: 421815; Command: fastqc; Return code: 0; Memory used: 0.161GB
> `FastQC report r2` fastqc/H9_PRO-seq_60_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_60/cutadapt/H9_PRO-seq_60.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/cutadapt/H9_PRO-seq_60.histogram`
> `fastq_pair -t 62490978 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_noadap.fastq` (421885)
Left paired: 17426433 Right paired: 17426433
Left single: 121333 Right single: 1607343
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_noadap.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_noadap.fastq.single.fq
Command completed. Elapsed time: 0:02:57. Running peak memory: 3.94GB.
PID: 421885; Command: fastq_pair; Return code: 0; Memory used: 3.94GB
> `flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_noadap.fastq.paired.fq -o H9_PRO-seq_60 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/cutadapt` (422539)
Command completed. Elapsed time: 0:00:39. Running peak memory: 3.94GB.
PID: 422539; Command: flash; Return code: 0; Memory used: 0.1GB
### Plot adapter insertion distribution (06-15 07:31:45) elapsed: 580.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/cutadapt/H9_PRO-seq_60_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_60/cutadapt/H9_PRO-seq_60.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/cutadapt -u 8` (422718)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.94GB.
PID: 422718; Command: Rscript; Return code: 0; Memory used: 0.201GB
> `Adapter insertion distribution` cutadapt/H9_PRO-seq_60_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_60_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_60/cutadapt/H9_PRO-seq_60.hist | awk 'BEGIN{max= 0; max_len=0; len=0}{if ($2>0+max) {max=$2; len=$1}; max_len=$1} END{print len-8}'`
> `Peak_adapter_insertion_size` 20 PEPPRO _RES_
Missing stat 'Degradation_ratio'
### Calculating degradation ratio (06-15 07:31:53) elapsed: 9.0 _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_60/cutadapt/H9_PRO-seq_60.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_60/cutadapt/H9_PRO-seq_60.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_60/cutadapt/H9_PRO-seq_60.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_60/cutadapt/H9_PRO-seq_60.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_60/cutadapt/H9_PRO-seq_60.hist`
> `Degradation_ratio` 1.0317 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed_dups.fastq`
> `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed_dups.fastq` (422754)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.94GB.
PID: 422754; 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_60/fastq/processed_R2.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/processed_R2.flag` (422789)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 422789; 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_60/fastq/repaired.flag`
> `fastq_pair -t 62490978 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq` (422790)
Left paired: 16863840 Right paired: 16863840
Left single: 133972 Right single: 1650293
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq.single.fq
Command completed. Elapsed time: 0:01:28. Running peak memory: 3.94GB.
PID: 422790; Command: fastq_pair; Return code: 0; Memory used: 3.399GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq` (422883)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 422883; Command: mv; Return code: 0; Memory used: 0.001GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq` (422884)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 422884; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/repaired.flag` (422886)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 422886; 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_60/fastq/dups_repaired.flag`
> `fastq_pair -t 62490978 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed_dups.fastq` (422888)
Left paired: 15645931 Right paired: 15645931
Left single: 100543 Right single: 2868202
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed_dups.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed_dups.fastq.single.fq
Command completed. Elapsed time: 0:01:30. Running peak memory: 3.94GB.
PID: 422888; Command: fastq_pair; Return code: 0; Memory used: 3.004GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_trimmed.fastq` (423331)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 423331; Command: mv; Return code: 0; Memory used: 0.001GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed_dups.fastq` (423334)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 423334; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/dups_repaired.flag` (423335)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 423335; Command: touch; Return code: 0; Memory used: 0.0GB
### Prealignments (06-15 07:35:13) elapsed: 200.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-15 07:35:13) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/human_rDNA_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/human_rDNA_bt2` (423337)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 423337; 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_60/prealignments/H9_PRO-seq_60_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_60/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_R2.fq` (423338)
> `(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id H9_PRO-seq_60 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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'
16863840 reads; of these:
16863840 (100.00%) were unpaired; of these:
15115450 (89.63%) aligned 0 times
1748390 (10.37%) aligned exactly 1 time
0 (0.00%) aligned >1 times
10.37% overall alignment rate
> `Aligned_reads_human_rDNA` 3496780.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 10.29 PEPPRO _RES_
### Map to human_rDNA (06-15 07:38:02) elapsed: 169.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/human_rDNA_dups_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/human_rDNA_dups_bt2` (423572)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 423572; Command: mkfifo; Return code: 0; Memory used: 0.0GB
File not added to cleanup: prealignments/human_rDNA_dups_bt2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_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_60/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_dups_R2.fq` (423573)
> `(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id H9_PRO-seq_60 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/fastq/H9_PRO-seq_60_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)`
not gzipping output
1748390 reads skipped
0 reads lost
File not added to cleanup: prealignments/human_rDNA_dups_bt2
### Map to genome (06-15 07:40:22) elapsed: 140.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_fail_qc_dups.bam
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort.bam`
> `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_60 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_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_60/aligned_hg38/tmpdb81hcn8 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp.bam` (423965,423966,423967)
1423235 reads skipped
0 reads lost
15115450 reads; of these:
15115450 (100.00%) were paired; of these:
6265719 (41.45%) aligned concordantly 0 times
7258222 (48.02%) aligned concordantly exactly 1 time
1591509 (10.53%) aligned concordantly >1 times
----
6265719 pairs aligned concordantly 0 times; of these:
1393636 (22.24%) aligned discordantly 1 time
----
4872083 pairs aligned 0 times concordantly or discordantly; of these:
9744166 mates make up the pairs; of these:
3999373 (41.04%) aligned 0 times
2100265 (21.55%) aligned exactly 1 time
3644528 (37.40%) aligned >1 times
86.77% overall alignment rate
[bam_sort_core] merging from 8 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:27:53. Running peak memory: 3.94GB.
PID: 423965; Command: bowtie2; Return code: 0; Memory used: 3.768GB
PID: 423966; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 423967; Command: samtools; Return code: 0; Memory used: 0.897GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort.bam` (426575)
Command completed. Elapsed time: 0:00:54. Running peak memory: 3.94GB.
PID: 426575; Command: samtools; Return code: 0; Memory used: 0.018GB
> `samtools depth -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 26231527 PEPPRO _RES_
> `QC_filtered_reads` 15331637 PEPPRO _RES_
> `Aligned_reads` 10899890.0 PEPPRO _RES_
> `Alignment_rate` 32.06 PEPPRO _RES_
> `Total_efficiency` 15.7 PEPPRO _RES_
> `Read_depth` 2.48 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort_dups.bam`
> `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_60 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_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_60/aligned_hg38/tmpdb81hcn8 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp_dups.bam` (428020,428021,428022)
14222696 reads; of these:
14222696 (100.00%) were paired; of these:
5772579 (40.59%) aligned concordantly 0 times
6946118 (48.84%) aligned concordantly exactly 1 time
1503999 (10.57%) aligned concordantly >1 times
----
5772579 pairs aligned concordantly 0 times; of these:
1336586 (23.15%) aligned discordantly 1 time
----
4435993 pairs aligned 0 times concordantly or discordantly; of these:
8871986 mates make up the pairs; of these:
3688993 (41.58%) aligned 0 times
2009280 (22.65%) aligned exactly 1 time
3173713 (35.77%) aligned >1 times
87.03% overall alignment rate
[bam_sort_core] merging from 8 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:25:20. Running peak memory: 3.94GB.
PID: 428020; Command: bowtie2; Return code: 0; Memory used: 3.755GB
PID: 428021; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 428022; Command: samtools; Return code: 0; Memory used: 0.896GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort_dups.bam` (431303)
Command completed. Elapsed time: 0:00:51. Running peak memory: 3.94GB.
PID: 431303; Command: samtools; Return code: 0; Memory used: 0.018GB
### Compress all unmapped read files (06-15 08:45:00) elapsed: 3878.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_R1.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_R1.fq` (431407)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.94GB.
PID: 431407; Command: pigz; Return code: 0; Memory used: 0.011GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_R2.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/prealignments/H9_PRO-seq_60_human_rDNA_unmap_R2.fq` (431647)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.94GB.
PID: 431647; Command: pigz; Return code: 0; Memory used: 0.009GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp.bam` (431684)
Command completed. Elapsed time: 0:00:22. Running peak memory: 3.94GB.
PID: 431684; Command: samtools; Return code: 0; Memory used: 0.015GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 504617 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort.bam` (431743)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.94GB.
PID: 431743; Command: samtools; Return code: 0; Memory used: 0.016GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_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_60/aligned_hg38/chr_sizes.bed` (432181,432182,432183,432184)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 432182; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 432184; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 432181; Command: samtools; Return code: 0; Memory used: 0.009GB
PID: 432183; 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_60/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_noMT.bam` (432186)
Command completed. Elapsed time: 0:00:23. Running peak memory: 3.94GB.
PID: 432186; Command: samtools; Return code: 0; Memory used: 0.019GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort.bam` (432238)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 432238; Command: mv; Return code: 0; Memory used: 0.001GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort.bam` (432239)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.94GB.
PID: 432239; Command: samtools; Return code: 0; Memory used: 0.016GB
### Split BAM file (06-15 08:46:47) elapsed: 108.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam` (432272,432273)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:30. Running peak memory: 3.94GB.
PID: 432272; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 432273; Command: samtools; Return code: 0; Memory used: 3.127GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE2.bam` (432399,432400)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:18. Running peak memory: 3.94GB.
PID: 432400; Command: samtools; Return code: 0; Memory used: 2.108GB
PID: 432399; Command: samtools; Return code: 0; Memory used: 0.004GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_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_60/aligned_hg38/H9_PRO-seq_60_temp_dups.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp_dups.bam` (432882)
Command completed. Elapsed time: 0:00:21. Running peak memory: 3.94GB.
PID: 432882; Command: samtools; Return code: 0; Memory used: 0.015GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_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_60/aligned_hg38/H9_PRO-seq_60_sort_dups.bam`
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort_dups.bam.bai
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_dups_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_dups_PE1.bam` (432926,432927)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:29. Running peak memory: 3.94GB.
PID: 432926; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 432927; Command: samtools; Return code: 0; Memory used: 3.072GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_dups_PE2.bam` (433155,433156)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:18. Running peak memory: 3.94GB.
PID: 433156; Command: samtools; Return code: 0; Memory used: 1.994GB
PID: 433155; Command: samtools; Return code: 0; Memory used: 0.004GB
### Calculate library complexity (06-15 08:53:19) elapsed: 392.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_preseq_out.txt`
> `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_dups_PE1.bam` (433796)
BAM_INPUT
TOTAL READS = 11393512
COUNTS_SUM = 11393512
DISTINCT READS = 9.6124e+06
DISTINCT COUNTS = 241
MAX COUNT = 17651
COUNTS OF 1 = 8.73782e+06
OBSERVED COUNTS (17652)
1 8737820
2 607973
3 135174
4 52518
5 25999
6 14941
7 9257
8 6177
9 4224
10 3156
11 2225
12 1814
13 1399
14 1174
15 964
16 755
17 655
18 539
19 508
20 399
21 362
22 317
23 308
24 251
25 230
26 198
27 167
28 150
29 130
30 155
31 135
32 118
33 135
34 119
35 93
36 93
37 98
38 76
39 66
40 69
41 73
42 54
43 56
44 65
45 34
46 34
47 35
48 37
49 39
50 40
51 28
52 36
53 39
54 29
55 29
56 28
57 32
58 32
59 28
60 21
61 16
62 31
63 26
64 13
65 19
66 17
67 14
68 14
69 8
70 11
71 9
72 13
73 13
74 11
75 10
76 16
77 13
78 7
79 13
80 12
81 4
82 7
83 8
84 11
85 6
86 7
87 10
88 12
89 10
90 7
91 5
92 7
93 2
94 12
95 5
96 5
97 8
98 4
99 4
100 4
101 2
102 1
103 2
104 10
105 7
106 6
107 3
108 4
109 5
110 3
111 3
112 3
113 6
114 2
115 3
116 5
117 2
118 2
119 6
120 3
121 1
123 6
124 3
125 6
126 5
127 2
128 3
129 6
130 1
131 4
132 3
133 2
134 1
135 4
136 1
137 2
139 1
140 6
141 2
142 1
143 4
145 1
147 1
149 1
150 1
153 2
154 1
155 1
156 1
157 3
158 2
159 1
160 1
161 1
162 1
163 1
164 1
165 1
166 1
167 1
168 1
169 1
170 2
172 1
173 1
175 2
177 2
178 1
181 2
182 1
187 1
192 1
193 2
194 1
196 1
197 2
198 1
199 1
200 1
201 1
202 2
203 2
204 1
207 5
209 1
213 1
214 1
215 1
217 1
220 1
222 1
225 1
229 2
231 2
235 1
238 1
250 1
258 1
262 1
263 1
268 1
271 1
288 1
295 1
298 1
305 1
306 1
323 2
325 1
327 1
330 1
341 1
347 1
373 1
423 1
432 2
434 1
436 1
437 2
546 1
551 1
577 1
598 1
637 1
726 1
811 1
815 1
1007 1
1173 1
1196 1
1220 1
1461 1
1489 1
1614 1
2162 1
2790 1
5627 1
6715 1
8463 1
17235 1
17651 1
sample size: 1000000
sample size: 2000000
sample size: 3000000
sample size: 4000000
sample size: 5000000
sample size: 6000000
sample size: 7000000
sample size: 8000000
sample size: 9000000
sample size: 10000000
sample size: 11000000
Command completed. Elapsed time: 0:01:01. Running peak memory: 3.94GB.
PID: 433796; 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_60/QC_hg38/H9_PRO-seq_60_preseq_yield.txt`
> `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_dups_PE1.bam` (433884)
BAM_INPUT
TOTAL READS = 11393512
DISTINCT READS = 9.6124e+06
DISTINCT COUNTS = 241
MAX COUNT = 17651
COUNTS OF 1 = 8.73782e+06
MAX TERMS = 100
OBSERVED COUNTS (17652)
1 8737820
2 607973
3 135174
4 52518
5 25999
6 14941
7 9257
8 6177
9 4224
10 3156
11 2225
12 1814
13 1399
14 1174
15 964
16 755
17 655
18 539
19 508
20 399
21 362
22 317
23 308
24 251
25 230
26 198
27 167
28 150
29 130
30 155
31 135
32 118
33 135
34 119
35 93
36 93
37 98
38 76
39 66
40 69
41 73
42 54
43 56
44 65
45 34
46 34
47 35
48 37
49 39
50 40
51 28
52 36
53 39
54 29
55 29
56 28
57 32
58 32
59 28
60 21
61 16
62 31
63 26
64 13
65 19
66 17
67 14
68 14
69 8
70 11
71 9
72 13
73 13
74 11
75 10
76 16
77 13
78 7
79 13
80 12
81 4
82 7
83 8
84 11
85 6
86 7
87 10
88 12
89 10
90 7
91 5
92 7
93 2
94 12
95 5
96 5
97 8
98 4
99 4
100 4
101 2
102 1
103 2
104 10
105 7
106 6
107 3
108 4
109 5
110 3
111 3
112 3
113 6
114 2
115 3
116 5
117 2
118 2
119 6
120 3
121 1
123 6
124 3
125 6
126 5
127 2
128 3
129 6
130 1
131 4
132 3
133 2
134 1
135 4
136 1
137 2
139 1
140 6
141 2
142 1
143 4
145 1
147 1
149 1
150 1
153 2
154 1
155 1
156 1
157 3
158 2
159 1
160 1
161 1
162 1
163 1
164 1
165 1
166 1
167 1
168 1
169 1
170 2
172 1
173 1
175 2
177 2
178 1
181 2
182 1
187 1
192 1
193 2
194 1
196 1
197 2
198 1
199 1
200 1
201 1
202 2
203 2
204 1
207 5
209 1
213 1
214 1
215 1
217 1
220 1
222 1
225 1
229 2
231 2
235 1
238 1
250 1
258 1
262 1
263 1
268 1
271 1
288 1
295 1
298 1
305 1
306 1
323 2
325 1
327 1
330 1
341 1
347 1
373 1
423 1
432 2
434 1
436 1
437 2
546 1
551 1
577 1
598 1
637 1
726 1
811 1
815 1
1007 1
1173 1
1196 1
1220 1
1461 1
1489 1
1614 1
2162 1
2790 1
5627 1
6715 1
8463 1
17235 1
17651 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
....................................................................................................
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]
Command completed. Elapsed time: 0:01:06. Running peak memory: 3.94GB.
PID: 433884; 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_60/QC_hg38/H9_PRO-seq_60_preseq_counts.txt`
> `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_preseq_counts.txt` (434152)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.94GB.
PID: 434152; Command: echo; Return code: 0; Memory used: 0.006GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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_60/QC_hg38/H9_PRO-seq_60_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_preseq_plot` (434189)
Processing H9_PRO-seq_60
INFO: Found real counts for H9_PRO-seq_60 - Total (M): 11.690255 Unique (M): 11.393512
Library complexity plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.94GB.
PID: 434189; Command: Rscript; Return code: 0; Memory used: 0.318GB
> `Library complexity` QC_hg38/H9_PRO-seq_60_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_60_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_60/QC_hg38/H9_PRO-seq_60_preseq_yield.txt | awk '{print $2}'`
> `Frac_exp_unique_at_10M` 0.8538 PEPPRO _RES_
### Calculate NRF, PBC1, and PBC2 (06-15 08:55:48) elapsed: 149.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam` (434208)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.94GB.
PID: 434208; Command: samtools; Return code: 0; Memory used: 0.01GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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_60/aligned_hg38/H9_PRO-seq_60_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_bamQC.tsv` (434216)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/tmp_H9_PRO-seq_60_PE1_petsiqdf'
Processing with 12 cores...
Discarding 103 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr14_GL000009v2_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_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_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', '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_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1']
Keeping 92 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Command completed. Elapsed time: 0:00:10. Running peak memory: 3.94GB.
PID: 434216; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.184GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_bamQC.tsv`
> `NRF` 1.0 PEPPRO _RES_
> `PBC1` 5845127.5 PEPPRO _RES_
> `PBC2` 5845127.5 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_unmap.bam`
> `samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_unmap.bam` (434279)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.94GB.
PID: 434279; Command: samtools; Return code: 0; Memory used: 0.009GB
> `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_temp.bam`
> `Unmapped_reads` 3999373 PEPPRO _RES_
### Split BAM by strand (06-15 08:56:18) elapsed: 29.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam` (434333)
Command completed. Elapsed time: 0:00:39. Running peak memory: 3.94GB.
PID: 434333; 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_60/aligned_hg38/H9_PRO-seq_60_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam` (434368)
Command completed. Elapsed time: 0:00:39. Running peak memory: 3.94GB.
PID: 434368; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-15 08:57:35) elapsed: 78.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (434425)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434425; Command: sed; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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_60/aligned_hg38/H9_PRO-seq_60_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_plus_TssEnrichment.txt` (434427)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.94GB.
PID: 434427; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.931GB
> `TSS_coding_score` 33.8 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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_60/aligned_hg38/H9_PRO-seq_60_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_minus_TssEnrichment.txt` (434464)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.94GB.
PID: 434464; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.953GB
> `TSS_non-coding_score` 12.3 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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_60/QC_hg38/H9_PRO-seq_60_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_minus_TssEnrichment.txt` (434495)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_minus_TssEnrichment.txt
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
TSS enrichment plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.94GB.
PID: 434495; Command: Rscript; Return code: 0; Memory used: 0.319GB
> `TSS enrichment` QC_hg38/H9_PRO-seq_60_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_60_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_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_60/QC_hg38/chr_order.txt` (434517,434518,434519,434520)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434517; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 434519; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 434518; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 434520; 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_60/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_keep.txt` (434522)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434522; Command: cut; Return code: 0; Memory used: 0.0GB
### Calculate Pause Index (PI) (06-15 08:57:52) elapsed: 17.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_ensembl_tss.bed` (434524,434525)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.94GB.
PID: 434524; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 434525; Command: bedtools; Return code: 0; Memory used: 0.096GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_ensembl_gene_body.bed` (434528,434529)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434528; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 434529; 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_60/QC_hg38/H9_PRO-seq_60_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/H9_PRO-seq_60_TSS_density.bed` (434531,434532,434533,434534)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.94GB.
PID: 434531; Command: bedtools; Return code: 0; Memory used: 0.007GB
PID: 434533; Command: sort; Return code: 0; Memory used: 0.009GB
PID: 434532; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 434534; Command: sort; Return code: 0; Memory used: 0.003GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_gene_body_density.bed` (434550,434551,434552)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.94GB.
PID: 434550; Command: bedtools; Return code: 0; Memory used: 0.071GB
PID: 434552; Command: sort; Return code: 0; Memory used: 0.009GB
PID: 434551; 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_60/QC_hg38/H9_PRO-seq_60_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_60/QC_hg38/H9_PRO-seq_60_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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_60/QC_hg38/tmp37n822fq` (434570,434571,434572)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434570; Command: join; Return code: 0; Memory used: 0.001GB
PID: 434572; Command: env; Return code: 0; Memory used: 0.004GB
PID: 434571; 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_60/QC_hg38/tmp37n822fq | 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_60/QC_hg38/H9_PRO-seq_60_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.0121273) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/tmp37n822fq > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_pause_index.bed` (434578)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434578; 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_60/QC_hg38/H9_PRO-seq_60_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` 33.82 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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_60/QC_hg38/H9_PRO-seq_60_pause_index.bed` (434583)
Pause index plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.94GB.
PID: 434583; Command: Rscript; Return code: 0; Memory used: 0.319GB
> `Pause index` QC_hg38/H9_PRO-seq_60_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_60_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_pause_index.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_pause_index.bed` (434604)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434604; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-15 08:58:32) elapsed: 40.0 _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_60/aligned_hg38/H9_PRO-seq_60_plus.bam`
10899890.0 4230357
> `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_60/aligned_hg38/H9_PRO-seq_60_minus.bam`
10899890.0 3944672
> `Minus_FRiP` 0.36 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_gene_sort.bed` (434658,434659)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 434658; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 434659; Command: bedtools; Return code: 0; Memory used: 0.004GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_gene_coverage.bed` (434661)
Command completed. Elapsed time: 0:00:18. Running peak memory: 3.94GB.
PID: 434661; Command: bedtools; Return code: 0; Memory used: 0.071GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/raw/hg38_annotations.bed.gz` (434680)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434680; Command: ln; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/hg38_annotations.bed` (434681)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434681; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 08:59:12) elapsed: 40.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/raw/hg38_annotations.bed` (434689)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 434689; 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_60/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Enhancer_sort.bed` (434691,434692,434693,434694)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 434691; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 434692; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 434694; Command: bedtools; Return code: 0; Memory used: 0.045GB
PID: 434693; 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_60/QC_hg38/H9_PRO-seq_60_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Enhancer_plus_coverage.bed` (434697)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.94GB.
PID: 434697; 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_60/QC_hg38/H9_PRO-seq_60_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Enhancer_minus_coverage.bed` (434705)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.94GB.
PID: 434705; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter_sort.bed` (434713,434714,434715,434716)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434713; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 434714; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 434716; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 434715; 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_60/QC_hg38/H9_PRO-seq_60_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Promoter_plus_coverage.bed` (434718)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.94GB.
PID: 434718; Command: bedtools; Return code: 0; Memory used: 0.017GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Promoter_minus_coverage.bed` (434727)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.94GB.
PID: 434727; Command: bedtools; Return code: 0; Memory used: 0.014GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter_Flanking_Region"` (434735)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 434735; 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_60/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter_Flanking_Region_sort.bed` (434736,434737,434738,434739)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 434736; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 434738; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 434737; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 434739; 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_60/QC_hg38/H9_PRO-seq_60_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Promoter_Flanking_Region_plus_coverage.bed` (434742)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.94GB.
PID: 434742; 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_60/QC_hg38/H9_PRO-seq_60_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Promoter_Flanking_Region_minus_coverage.bed` (434751)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.94GB.
PID: 434751; Command: bedtools; Return code: 0; Memory used: 0.015GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/5_UTR"` (435030)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 435030; 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_60/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/5_UTR_sort.bed` (435031,435032,435033,435034)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 435031; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 435032; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 435034; Command: bedtools; Return code: 0; Memory used: 0.03GB
PID: 435033; 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_60/QC_hg38/H9_PRO-seq_60_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_5_UTR_plus_coverage.bed` (435036)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.94GB.
PID: 435036; 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_60/QC_hg38/H9_PRO-seq_60_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_5_UTR_minus_coverage.bed` (435058)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.94GB.
PID: 435058; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/3_UTR"` (435091)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 435091; 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_60/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/3_UTR_sort.bed` (435092,435093,435094,435095)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 435092; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 435093; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 435095; Command: bedtools; Return code: 0; Memory used: 0.034GB
PID: 435094; 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_60/QC_hg38/H9_PRO-seq_60_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_3_UTR_plus_coverage.bed` (435098)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.94GB.
PID: 435098; 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_60/QC_hg38/H9_PRO-seq_60_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_3_UTR_minus_coverage.bed` (435107)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.94GB.
PID: 435107; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Exon_sort.bed` (435131,435132,435133,435134)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.94GB.
PID: 435131; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 435132; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 435134; Command: bedtools; Return code: 0; Memory used: 0.17GB
PID: 435133; 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_60/QC_hg38/H9_PRO-seq_60_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Exon_plus_coverage.bed` (435138)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.94GB.
PID: 435138; Command: bedtools; Return code: 0; Memory used: 0.018GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Exon_minus_coverage.bed` (435147)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.94GB.
PID: 435147; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Intron_sort.bed` (435155,435156,435157,435158)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 435155; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 435157; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 435156; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 435158; Command: bedtools; Return code: 0; Memory used: 0.082GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Intron_plus_coverage.bed` (435161)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.94GB.
PID: 435161; Command: bedtools; Return code: 0; Memory used: 0.022GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Intron_minus_coverage.bed` (435183)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.94GB.
PID: 435183; Command: bedtools; Return code: 0; Memory used: 0.026GB
### Plot cFRiF/FRiF (06-15 09:01:13) elapsed: 121.0 _TIME_
> `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_60 -z 3099922541 -n 5966715 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Intron_plus_coverage.bed` (435206)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:35. Running peak memory: 3.94GB.
PID: 435206; Command: Rscript; Return code: 0; Memory used: 0.466GB
> `cFRiF` QC_hg38/H9_PRO-seq_60_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_60_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_60 -z 3099922541 -n 5966715 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_Intron_plus_coverage.bed` (435273)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:24. Running peak memory: 3.94GB.
PID: 435273; Command: Rscript; Return code: 0; Memory used: 0.517GB
> `FRiF` QC_hg38/H9_PRO-seq_60_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_60_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-15 09:02:13) elapsed: 60.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_exons_sort.bed` (435305,435306)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.94GB.
PID: 435306; Command: bedtools; Return code: 0; Memory used: 0.096GB
PID: 435305; Command: grep; Return code: 0; Memory used: 0.004GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/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_60/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_introns_sort.bed` (435312,435313,435314)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.94GB.
PID: 435312; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 435314; Command: bedtools; Return code: 0; Memory used: 0.005GB
PID: 435313; Command: bedtools; Return code: 0; Memory used: 0.036GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_exons_coverage.bed` (435320)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.94GB.
PID: 435320; Command: bedtools; Return code: 0; Memory used: 0.013GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_introns_coverage.bed` (435333)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.94GB.
PID: 435333; Command: bedtools; Return code: 0; Memory used: 0.061GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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]/10.89989)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_exons_rpkm.bed` (435348,435349,435350)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 435348; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 435350; Command: sort; Return code: 0; Memory used: 0.003GB
PID: 435349; 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_60/QC_hg38/H9_PRO-seq_60_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]/10.89989)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_introns_rpkm.bed` (435352,435353,435354)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.94GB.
PID: 435352; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 435354; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 435353; 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_60/QC_hg38/H9_PRO-seq_60_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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_60/QC_hg38/H9_PRO-seq_60_exon_intron_ratios.bed` (435358,435359,435360)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 435358; Command: join; Return code: 0; Memory used: 0.001GB
PID: 435360; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 435359; 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_60/QC_hg38/H9_PRO-seq_60_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` 1.29 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_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_60/QC_hg38/H9_PRO-seq_60_exon_intron_ratios.bed --annotate` (435366)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.94GB.
PID: 435366; Command: Rscript; Return code: 0; Memory used: 0.32GB
> `mRNA contamination` QC_hg38/H9_PRO-seq_60_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_60_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_exon_intron_ratios.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/QC_hg38/H9_PRO-seq_60_exon_intron_ratios.bed` (435387)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.94GB.
PID: 435387; Command: pigz; Return code: 0; Memory used: 0.005GB
### Produce bigWig files (06-15 09:02:59) elapsed: 46.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_plus.bam` (435395)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.94GB.
PID: 435395; Command: samtools; Return code: 0; Memory used: 0.012GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_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_60/signal_hg38/H9_PRO-seq_60_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 10899890.0` (435400)
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_60/aligned_hg38/H9_PRO-seq_60_plus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_60_plus_cuttrace_rdcn1r3e'
Processing with 4 cores...
stdin is empty of data
Discarding 120 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270710v1_random', 'chr1_KI270714v1_random', 'chr2_KI270715v1_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr14_GL000009v2_random', 'chr14_KI270725v1_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_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_GL000226v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1']
Keeping 75 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_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 75 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_plus_exact_body_0-mer.bw'
Merging 75 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:06:14. Running peak memory: 3.94GB.
PID: 435400; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.406GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_minus.bam` (436902)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.94GB.
PID: 436902; Command: samtools; Return code: 0; Memory used: 0.012GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/aligned_hg38/H9_PRO-seq_60_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_60/signal_hg38/H9_PRO-seq_60_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 10899890.0` (436907)
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_60/aligned_hg38/H9_PRO-seq_60_minus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_60_minus_cuttrace_7wun9_4b'
Processing with 4 cores...
stdin is empty of data
Discarding 116 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr14_KI270723v1_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_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_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1']
Keeping 79 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 79 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_minus_exact_body_0-mer.bw'
Merging 79 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_60/signal_hg38/H9_PRO-seq_60_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:06:07. Running peak memory: 3.94GB.
PID: 436907; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.654GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 1:58:11
* Total elapsed time (all runs): 3:23:31
* Peak memory (this run): 3.9404 GB
* Pipeline completed time: 2020-06-15 09:15:29