### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_40 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 8 -M 10000 --input2 /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-aw29-20b
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/
* 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`: `8`
* `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_40pct_PE1.fastq.gz']`
* `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE2.fastq.gz']`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `10000`
* `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_40`
* `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_40pct_PE1.fastq.gz
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE2.fastq.gz
> `File_mb` 971.29 PEPPRO _RES_
> `Read_type` PAIRED PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-15 07:17:19) elapsed: 1.0 _TIME_
Number of input file sets: 2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R1.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R1.fastq.gz` (12548)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 12548; 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_40/raw/H9_PRO-seq_40_R1.fastq.gz'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R2.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R2.fastq.gz` (12549)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 12549; 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_40/raw/H9_PRO-seq_40_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_40/fastq/H9_PRO-seq_40_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2.fastq`
> `pigz -f -p 8 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1.fastq` (12550)
Command completed. Elapsed time: 0:00:29. Running peak memory: 0.002GB.
PID: 12550; Command: pigz; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 8 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2.fastq` (12583)
Command completed. Elapsed time: 0:00:30. Running peak memory: 0.002GB.
PID: 12583; Command: pigz; Return code: 0; Memory used: 0.002GB
> `Raw_reads` 46292984 PEPPRO _RES_
> `Fastq_reads` 46292984 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R2.fastq.gz']
### FASTQ processing: (06-15 07:18:37) elapsed: 78.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq`
> `(cutadapt -j 8 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40_R1_cutadapt.txt` (12654)
Command completed. Elapsed time: 0:00:45. Running peak memory: 1.598GB.
PID: 12654; Command: cutadapt; Return code: 0; Memory used: 1.598GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq` (12712,12713)
Command completed. Elapsed time: 0:00:17. Running peak memory: 1.598GB.
PID: 12712; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 12713; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 11331720 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_40/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq` (12734)
Started analysis of H9_PRO-seq_40_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 20% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 25% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 35% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_40_R1_processed.fastq
Analysis complete for H9_PRO-seq_40_R1_processed.fastq
Command completed. Elapsed time: 0:00:30. Running peak memory: 1.598GB.
PID: 12734; Command: fastqc; Return code: 0; Memory used: 0.169GB
> `FastQC report r1` fastqc/H9_PRO-seq_40_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_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq`
> `seqkit rmdup --threads 8 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq` (13017)
[INFO][0m 691509 duplicated records removed
Command completed. Elapsed time: 0:00:19. Running peak memory: 1.598GB.
PID: 13017; Command: seqkit; Return code: 0; Memory used: 1.032GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq` (13051,13052)
Command completed. Elapsed time: 0:00:13. Running peak memory: 1.598GB.
PID: 13051; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 13052; 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_40/cutadapt/H9_PRO-seq_40_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 18342898.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40_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_40/cutadapt/H9_PRO-seq_40_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 11448553.0 PEPPRO _RES_
> `Duplicate_reads` 691509.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 49.4613 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/processed_R1.flag` (13104)
Command completed. Elapsed time: 0:00:00. Running peak memory: 1.598GB.
PID: 13104; 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_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq`
> `(cutadapt -j 8 -m 10 -O 1 -a GATCGTCGGACTGTAGAACTCTGAAC /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40_R2_cutadapt.txt` (13106)
Command completed. Elapsed time: 0:00:42. Running peak memory: 1.598GB.
PID: 13106; Command: cutadapt; Return code: 0; Memory used: 1.093GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq` (13161,13162)
Command completed. Elapsed time: 0:00:14. Running peak memory: 1.598GB.
PID: 13161; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 13162; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 22663440 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_40/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq` (13218)
Started analysis of H9_PRO-seq_40_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 20% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 25% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 35% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_40_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_40_R1_processed.fastq
Analysis complete for H9_PRO-seq_40_R1_processed.fastq
Command completed. Elapsed time: 0:00:28. Running peak memory: 1.598GB.
PID: 13218; Command: fastqc; Return code: 0; Memory used: 0.169GB
> `FastQC report r1` fastqc/H9_PRO-seq_40_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_40/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq` (13257)
Started analysis of H9_PRO-seq_40_R2_trimmed.fastq
Approx 5% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 10% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 15% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 20% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 25% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 30% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 35% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 40% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 45% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 50% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 55% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 60% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 65% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 70% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 75% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 80% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 85% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 90% complete for H9_PRO-seq_40_R2_trimmed.fastq
Approx 95% complete for H9_PRO-seq_40_R2_trimmed.fastq
Analysis complete for H9_PRO-seq_40_R2_trimmed.fastq
Command completed. Elapsed time: 0:00:26. Running peak memory: 1.598GB.
PID: 13257; Command: fastqc; Return code: 0; Memory used: 0.164GB
> `FastQC report r2` fastqc/H9_PRO-seq_40_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_40/cutadapt/H9_PRO-seq_40.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40.histogram`
> `fastq_pair -t 41663685 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq` (13327)
Left paired: 11616977 Right paired: 11616977
Left single: 80962 Right single: 1072452
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq.single.fq
Command completed. Elapsed time: 0:01:12. Running peak memory: 2.274GB.
PID: 13327; Command: fastq_pair; Return code: 0; Memory used: 2.274GB
> `flash -q -t 8 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq.paired.fq -o H9_PRO-seq_40 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt` (13389)
Command completed. Elapsed time: 0:00:36. Running peak memory: 2.274GB.
PID: 13389; Command: flash; Return code: 0; Memory used: 0.067GB
### Plot adapter insertion distribution (06-15 07:24:55) elapsed: 377.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40_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_40/cutadapt/H9_PRO-seq_40.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt -u 8` (13560)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:08. Running peak memory: 2.274GB.
PID: 13560; Command: Rscript; Return code: 0; Memory used: 0.122GB
> `Adapter insertion distribution` cutadapt/H9_PRO-seq_40_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_40_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_40/cutadapt/H9_PRO-seq_40.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 07:25:03) elapsed: 8.0 _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_40/cutadapt/H9_PRO-seq_40.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_40/cutadapt/H9_PRO-seq_40.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_40/cutadapt/H9_PRO-seq_40.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_40/cutadapt/H9_PRO-seq_40.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_40/cutadapt/H9_PRO-seq_40.hist`
> `Degradation_ratio` 1.0318 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq`
> `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq` (13793)
Command completed. Elapsed time: 0:00:05. Running peak memory: 2.274GB.
PID: 13793; 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_40/fastq/processed_R2.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/processed_R2.flag` (13800)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.274GB.
PID: 13800; 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_40/fastq/repaired.flag`
> `fastq_pair -t 41663685 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq` (13801)
Left paired: 11242330 Right paired: 11242330
Left single: 89390 Right single: 1100903
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq.single.fq
Command completed. Elapsed time: 0:01:01. Running peak memory: 2.361GB.
PID: 13801; Command: fastq_pair; Return code: 0; Memory used: 2.361GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq` (13855)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.361GB.
PID: 13855; Command: mv; Return code: 0; Memory used: 0.002GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq` (13856)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.361GB.
PID: 13856; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/repaired.flag` (13857)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.361GB.
PID: 13857; 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_40/fastq/dups_repaired.flag`
> `fastq_pair -t 41663685 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq` (13858)
Left paired: 10608843 Right paired: 10608843
Left single: 68392 Right single: 1734390
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq.single.fq
Command completed. Elapsed time: 0:00:54. Running peak memory: 2.428GB.
PID: 13858; Command: fastq_pair; Return code: 0; Memory used: 2.428GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq` (13906)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB.
PID: 13906; Command: mv; Return code: 0; Memory used: 0.001GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq` (13907)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB.
PID: 13907; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/dups_repaired.flag` (13909)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB.
PID: 13909; Command: touch; Return code: 0; Memory used: 0.0GB
### Prealignments (06-15 07:27:05) elapsed: 122.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-15 07:27:05) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_bt2` (13910)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB.
PID: 13910; Command: mkfifo; Return code: 0; Memory used: 0.001GB
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_40/prealignments/H9_PRO-seq_40_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_40/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R2.fq` (13911)
> `(bowtie2 -p 8 -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_40 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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'
11242330 reads; of these:
11242330 (100.00%) were unpaired; of these:
10076783 (89.63%) aligned 0 times
1165547 (10.37%) aligned exactly 1 time
0 (0.00%) aligned >1 times
10.37% overall alignment rate
> `Aligned_reads_human_rDNA` 2331094.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 10.29 PEPPRO _RES_
### Map to human_rDNA (06-15 07:28:25) elapsed: 81.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_dups_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_dups_bt2` (13995)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB.
PID: 13995; Command: mkfifo; Return code: 0; Memory used: 0.002GB
File not added to cleanup: prealignments/human_rDNA_dups_bt2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_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_40/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_dups_R2.fq` (13996)
> `(bowtie2 -p 8 -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_40 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)`
not gzipping output
1165547 reads skipped
0 reads lost
File not added to cleanup: prealignments/human_rDNA_dups_bt2
### Map to genome (06-15 07:29:56) elapsed: 90.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_fail_qc_dups.bam
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam`
> `bowtie2 -p 8 --very-sensitive -X 2000 --rg-id H9_PRO-seq_40 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_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_40/aligned_hg38/tmpa7932xtf -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam` (14082,14083,14084)
982150 reads skipped
0 reads lost
10076783 reads; of these:
10076783 (100.00%) were paired; of these:
4178107 (41.46%) aligned concordantly 0 times
4837452 (48.01%) aligned concordantly exactly 1 time
1061224 (10.53%) aligned concordantly >1 times
----
4178107 pairs aligned concordantly 0 times; of these:
929745 (22.25%) aligned discordantly 1 time
----
3248362 pairs aligned 0 times concordantly or discordantly; of these:
6496724 mates make up the pairs; of these:
2667586 (41.06%) aligned 0 times
1399857 (21.55%) aligned exactly 1 time
2429281 (37.39%) aligned >1 times
86.76% overall alignment rate
[bam_sort_core] merging from 5 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:25:17. Running peak memory: 3.662GB.
PID: 14083; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 14082; Command: bowtie2; Return code: 0; Memory used: 3.662GB
PID: 14084; Command: samtools; Return code: 0; Memory used: 0.896GB
> `samtools view -q 10 -b -@ 8 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam` (16987)
Command completed. Elapsed time: 0:00:39. Running peak memory: 3.662GB.
PID: 16987; Command: samtools; Return code: 0; Memory used: 0.015GB
> `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_40/aligned_hg38/H9_PRO-seq_40_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 17485980 PEPPRO _RES_
> `QC_filtered_reads` 10220292 PEPPRO _RES_
> `Aligned_reads` 7265688.5 PEPPRO _RES_
> `Alignment_rate` 32.06 PEPPRO _RES_
> `Total_efficiency` 15.7 PEPPRO _RES_
> `Read_depth` 2.14 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam`
> `bowtie2 -p 8 --very-sensitive -X 2000 --rg-id H9_PRO-seq_40 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_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_40/aligned_hg38/tmpa7932xtf -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp_dups.bam` (17690,17695,17696)
9626693 reads; of these:
9626693 (100.00%) were paired; of these:
3912255 (40.64%) aligned concordantly 0 times
4695529 (48.78%) aligned concordantly exactly 1 time
1018909 (10.58%) aligned concordantly >1 times
----
3912255 pairs aligned concordantly 0 times; of these:
903759 (23.10%) aligned discordantly 1 time
----
3008496 pairs aligned 0 times concordantly or discordantly; of these:
6016992 mates make up the pairs; of these:
2491165 (41.40%) aligned 0 times
1357608 (22.56%) aligned exactly 1 time
2168219 (36.03%) aligned >1 times
87.06% overall alignment rate
[bam_sort_core] merging from 5 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:23:59. Running peak memory: 3.662GB.
PID: 17690; Command: bowtie2; Return code: 0; Memory used: 3.65GB
PID: 17695; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 17696; Command: samtools; Return code: 0; Memory used: 0.896GB
> `samtools view -q 10 -b -@ 8 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam` (20007)
Command completed. Elapsed time: 0:00:37. Running peak memory: 3.662GB.
PID: 20007; Command: samtools; Return code: 0; Memory used: 0.015GB
### Compress all unmapped read files (06-15 08:27:43) elapsed: 3468.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R1.fq.gz`
> `pigz -f -p 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R1.fq` (20054)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.662GB.
PID: 20054; Command: pigz; Return code: 0; Memory used: 0.006GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R2.fq.gz`
> `pigz -f -p 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R2.fq` (20078)
Command completed. Elapsed time: 0:00:13. Running peak memory: 3.662GB.
PID: 20078; Command: pigz; Return code: 0; Memory used: 0.006GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam` (20099)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.662GB.
PID: 20099; Command: samtools; Return code: 0; Memory used: 0.018GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 336077 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam` (20117)
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.662GB.
PID: 20117; Command: samtools; Return code: 0; Memory used: 0.008GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/aligned_hg38/chr_sizes.bed` (20127,20128,20129,20130)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 20128; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 20130; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 20127; Command: samtools; Return code: 0; Memory used: 0.01GB
PID: 20129; 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_40/aligned_hg38/chr_sizes.bed -b -@ 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_noMT.bam` (20132)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.662GB.
PID: 20132; Command: samtools; Return code: 0; Memory used: 0.016GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam` (20158)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 20158; Command: mv; Return code: 0; Memory used: 0.001GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam` (20159)
Command completed. Elapsed time: 0:00:11. Running peak memory: 3.662GB.
PID: 20159; Command: samtools; Return code: 0; Memory used: 0.008GB
### Split BAM file (06-15 08:29:06) elapsed: 83.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam | samtools sort - -@ 8 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam` (20169,20170)
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Command completed. Elapsed time: 0:01:06. Running peak memory: 3.662GB.
PID: 20169; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 20170; Command: samtools; Return code: 0; Memory used: 2.08GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam | samtools sort - -@ 8 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE2.bam` (20511,20512)
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Command completed. Elapsed time: 0:00:55. Running peak memory: 3.662GB.
PID: 20511; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 20512; Command: samtools; Return code: 0; Memory used: 1.665GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_temp_dups.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp_dups.bam` (20612)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.662GB.
PID: 20612; Command: samtools; Return code: 0; Memory used: 0.019GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam`
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam.bai
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam | samtools sort - -@ 8 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam` (20630,20631)
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Command completed. Elapsed time: 0:01:05. Running peak memory: 3.662GB.
PID: 20630; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 20631; Command: samtools; Return code: 0; Memory used: 2.058GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam | samtools sort - -@ 8 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE2.bam` (20711,20712)
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Command completed. Elapsed time: 0:00:55. Running peak memory: 3.662GB.
PID: 20711; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 20712; Command: samtools; Return code: 0; Memory used: 1.648GB
### Calculate library complexity (06-15 08:33:47) elapsed: 281.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_out.txt`
> `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam` (20786)
BAM_INPUT
TOTAL READS = 7703559
COUNTS_SUM = 7703559
DISTINCT READS = 6.71206e+06
DISTINCT COUNTS = 185
MAX COUNT = 13085
COUNTS OF 1 = 6.20795e+06
OBSERVED COUNTS (13086)
1 6207952
2 358767
3 75714
4 28508
5 14029
6 7631
7 4735
8 3035
9 2128
10 1643
11 1174
12 916
13 690
14 602
15 507
16 401
17 353
18 333
19 270
20 213
21 177
22 163
23 157
24 134
25 146
26 121
27 103
28 88
29 88
30 64
31 55
32 80
33 58
34 53
35 43
36 36
37 46
38 47
39 39
40 41
41 33
42 34
43 27
44 21
45 15
46 24
47 31
48 24
49 22
50 12
51 21
52 16
53 25
54 9
55 14
56 10
57 16
58 16
59 15
60 10
61 7
62 10
63 9
64 10
65 7
66 8
67 4
68 12
69 11
70 8
71 5
72 4
73 4
74 5
75 5
76 3
77 5
78 4
79 3
80 7
81 5
82 4
83 6
84 5
85 3
86 5
87 3
88 10
89 3
90 4
91 7
92 2
93 6
95 2
96 5
97 4
99 2
100 1
101 1
102 2
103 3
104 1
105 4
106 2
107 3
109 1
110 2
111 3
112 1
113 1
114 2
118 1
120 2
121 2
122 1
123 1
124 1
125 3
126 3
128 3
129 2
130 1
132 2
133 2
135 1
137 1
139 2
140 3
141 2
143 1
145 1
148 2
150 1
151 1
152 2
154 1
155 1
158 1
161 1
163 1
165 1
170 2
171 1
174 1
188 1
190 1
201 1
206 1
209 1
211 2
215 1
219 2
221 1
222 1
223 1
231 1
242 1
275 1
283 1
284 1
287 1
288 2
289 1
374 1
375 1
377 1
448 1
473 1
491 1
545 1
572 1
677 1
827 1
831 1
833 1
1005 1
1061 1
1083 1
1493 1
1906 1
3867 1
4608 1
5719 1
12251 1
13085 1
sample size: 1000000
sample size: 2000000
sample size: 3000000
sample size: 4000000
sample size: 5000000
sample size: 6000000
sample size: 7000000
Command completed. Elapsed time: 0:00:42. Running peak memory: 3.662GB.
PID: 20786; 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_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt`
> `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam` (20822)
BAM_INPUT
TOTAL READS = 7703559
DISTINCT READS = 6.71206e+06
DISTINCT COUNTS = 185
MAX COUNT = 13085
COUNTS OF 1 = 6.20795e+06
MAX TERMS = 92
OBSERVED COUNTS (13086)
1 6207952
2 358767
3 75714
4 28508
5 14029
6 7631
7 4735
8 3035
9 2128
10 1643
11 1174
12 916
13 690
14 602
15 507
16 401
17 353
18 333
19 270
20 213
21 177
22 163
23 157
24 134
25 146
26 121
27 103
28 88
29 88
30 64
31 55
32 80
33 58
34 53
35 43
36 36
37 46
38 47
39 39
40 41
41 33
42 34
43 27
44 21
45 15
46 24
47 31
48 24
49 22
50 12
51 21
52 16
53 25
54 9
55 14
56 10
57 16
58 16
59 15
60 10
61 7
62 10
63 9
64 10
65 7
66 8
67 4
68 12
69 11
70 8
71 5
72 4
73 4
74 5
75 5
76 3
77 5
78 4
79 3
80 7
81 5
82 4
83 6
84 5
85 3
86 5
87 3
88 10
89 3
90 4
91 7
92 2
93 6
95 2
96 5
97 4
99 2
100 1
101 1
102 2
103 3
104 1
105 4
106 2
107 3
109 1
110 2
111 3
112 1
113 1
114 2
118 1
120 2
121 2
122 1
123 1
124 1
125 3
126 3
128 3
129 2
130 1
132 2
133 2
135 1
137 1
139 2
140 3
141 2
143 1
145 1
148 2
150 1
151 1
152 2
154 1
155 1
158 1
161 1
163 1
165 1
170 2
171 1
174 1
188 1
190 1
201 1
206 1
209 1
211 2
215 1
219 2
221 1
222 1
223 1
231 1
242 1
275 1
283 1
284 1
287 1
288 2
289 1
374 1
375 1
377 1
448 1
473 1
491 1
545 1
572 1
677 1
827 1
831 1
833 1
1005 1
1061 1
1083 1
1493 1
1906 1
3867 1
4608 1
5719 1
12251 1
13085 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
..............._.................................._...................................................
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]
Command completed. Elapsed time: 0:00:46. Running peak memory: 3.662GB.
PID: 20822; Command: preseq; Return code: 0; Memory used: 0.011GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_counts.txt`
> `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_counts.txt` (21058)
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.662GB.
PID: 21058; 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_40/QC_hg38/H9_PRO-seq_40_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_plot` (21073)
Processing H9_PRO-seq_40
INFO: Found real counts for H9_PRO-seq_40 - Total (M): 7.79292 Unique (M): 7.703559
Library complexity plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21073; Command: Rscript; Return code: 0; Memory used: 0.204GB
> `Library complexity` QC_hg38/H9_PRO-seq_40_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt | awk '{print $2}'`
> `Frac_exp_unique_at_10M` 0.8539 PEPPRO _RES_
### Calculate NRF, PBC1, and PBC2 (06-15 08:35:33) elapsed: 106.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam` (21093)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21093; Command: samtools; Return code: 0; Memory used: 0.011GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -c 8 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_bamQC.tsv` (21104)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/tmp_H9_PRO-seq_40_PE1_n6fxgr9j'
Processing with 8 cores...
Discarding 106 chunk(s) of reads: ['chrM', 'chr1_KI270708v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr9_KI270720v1_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_KI270745v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1']
Keeping 89 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_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', '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_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: 0:00:11. Running peak memory: 3.662GB.
PID: 21104; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 0.84GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_bamQC.tsv`
> `NRF` 1.0 PEPPRO _RES_
> `PBC1` 3896460.0 PEPPRO _RES_
> `PBC2` 3896460.0 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_unmap.bam`
> `samtools view -b -@ 8 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_unmap.bam` (21161)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.662GB.
PID: 21161; Command: samtools; Return code: 0; Memory used: 0.013GB
> `samtools view -c -f 4 -@ 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam`
> `Unmapped_reads` 2667586 PEPPRO _RES_
### Split BAM by strand (06-15 08:35:58) elapsed: 24.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam` (21190)
Command completed. Elapsed time: 0:00:29. Running peak memory: 3.662GB.
PID: 21190; 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_40/aligned_hg38/H9_PRO-seq_40_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam` (21215)
Command completed. Elapsed time: 0:00:28. Running peak memory: 3.662GB.
PID: 21215; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-15 08:36:55) elapsed: 57.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (21242)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21242; Command: sed; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/plus_TSS.tsv -p ends -c 8 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_plus_TssEnrichment.txt` (21243)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB.
PID: 21243; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.567GB
> `TSS_coding_score` 33.6 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/minus_TSS.tsv -p ends -c 8 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_minus_TssEnrichment.txt` (21266)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB.
PID: 21266; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.695GB
> `TSS_non-coding_score` 12.3 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_minus_TssEnrichment.txt` (21288)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_minus_TssEnrichment.txt
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
TSS enrichment plot completed!
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.662GB.
PID: 21288; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `TSS enrichment` QC_hg38/H9_PRO-seq_40_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_40_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/QC_hg38/chr_order.txt` (21309,21310,21311,21312)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21309; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 21311; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 21310; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 21312; 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_40/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_keep.txt` (21314)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21314; Command: cut; Return code: 0; Memory used: 0.0GB
### Calculate Pause Index (PI) (06-15 08:37:12) elapsed: 17.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_tss.bed` (21316,21317)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.662GB.
PID: 21316; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 21317; Command: bedtools; Return code: 0; Memory used: 0.093GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_gene_body.bed` (21321,21322)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21321; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 21322; 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_40/QC_hg38/H9_PRO-seq_40_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/H9_PRO-seq_40_TSS_density.bed` (21324,21325,21326,21327)
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.662GB.
PID: 21326; Command: sort; Return code: 0; Memory used: 0.008GB
PID: 21324; Command: bedtools; Return code: 0; Memory used: 0.007GB
PID: 21327; Command: sort; Return code: 0; Memory used: 0.003GB
PID: 21325; 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_40/QC_hg38/H9_PRO-seq_40_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_gene_body_density.bed` (21339,21340,21341)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.662GB.
PID: 21339; Command: bedtools; Return code: 0; Memory used: 0.055GB
PID: 21341; Command: sort; Return code: 0; Memory used: 0.005GB
PID: 21340; 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_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/tmp2cnv4nn_` (21356,21357,21358)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21356; Command: join; Return code: 0; Memory used: 0.001GB
PID: 21358; Command: env; Return code: 0; Memory used: 0.004GB
PID: 21357; 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_40/QC_hg38/tmp2cnv4nn_ | 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_40/QC_hg38/H9_PRO-seq_40_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.0086562) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/tmp2cnv4nn_ > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_pause_index.bed` (21364)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21364; 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_40/QC_hg38/H9_PRO-seq_40_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` 33.24 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_pause_index.bed` (21369)
Pause index plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB.
PID: 21369; Command: Rscript; Return code: 0; Memory used: 0.296GB
> `Pause index` QC_hg38/H9_PRO-seq_40_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_40_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_pause_index.bed.gz`
> `pigz -f -p 8 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_pause_index.bed` (21388)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21388; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-15 08:37:48) elapsed: 36.0 _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_40/aligned_hg38/H9_PRO-seq_40_plus.bam`
7265688.5 2820700
> `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_40/aligned_hg38/H9_PRO-seq_40_minus.bam`
7265688.5 2629275
> `Minus_FRiP` 0.36 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_gene_sort.bed` (21418,21419)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB.
PID: 21418; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 21419; Command: bedtools; Return code: 0; Memory used: 0.005GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_gene_coverage.bed` (21422)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.662GB.
PID: 21422; Command: bedtools; Return code: 0; Memory used: 0.055GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/raw/hg38_annotations.bed.gz` (21437)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21437; Command: ln; Return code: 0; Memory used: 0.0GB
> `pigz -f -p 8 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/hg38_annotations.bed` (21438)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21438; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 08:38:19) elapsed: 31.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/hg38_annotations.bed` (21446)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB.
PID: 21446; 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_40/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Enhancer_sort.bed` (21449,21450,21451,21452)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB.
PID: 21449; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 21450; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 21452; Command: bedtools; Return code: 0; Memory used: 0.044GB
PID: 21451; 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_40/QC_hg38/H9_PRO-seq_40_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Enhancer_plus_coverage.bed` (21454)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21454; 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_40/QC_hg38/H9_PRO-seq_40_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Enhancer_minus_coverage.bed` (21461)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB.
PID: 21461; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_sort.bed` (21467,21468,21469,21470)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21467; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 21468; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 21470; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 21469; 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_40/QC_hg38/H9_PRO-seq_40_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_plus_coverage.bed` (21472)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21472; Command: bedtools; Return code: 0; Memory used: 0.013GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_minus_coverage.bed` (21479)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21479; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region"` (21485)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21485; 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_40/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region_sort.bed` (21486,21487,21488,21489)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB.
PID: 21486; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 21488; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 21487; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 21489; Command: bedtools; Return code: 0; Memory used: 0.048GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_plus_coverage.bed` (21492)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21492; 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_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_minus_coverage.bed` (21499)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21499; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR"` (21505)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21505; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR_sort.bed` (21507,21508,21509,21510)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB.
PID: 21507; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 21508; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 21510; Command: bedtools; Return code: 0; Memory used: 0.01GB
PID: 21509; 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_40/QC_hg38/H9_PRO-seq_40_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_5_UTR_plus_coverage.bed` (21512)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21512; 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_40/QC_hg38/H9_PRO-seq_40_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_5_UTR_minus_coverage.bed` (21519)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB.
PID: 21519; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR"` (21525)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21525; Command: mv; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR_sort.bed` (21526,21527,21528,21529)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB.
PID: 21526; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 21527; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 21529; Command: bedtools; Return code: 0; Memory used: 0.01GB
PID: 21528; 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_40/QC_hg38/H9_PRO-seq_40_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_3_UTR_plus_coverage.bed` (21531)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21531; 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_40/QC_hg38/H9_PRO-seq_40_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_3_UTR_minus_coverage.bed` (21539)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB.
PID: 21539; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon_sort.bed` (21546,21547,21548,21549)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.662GB.
PID: 21546; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 21547; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 21549; Command: bedtools; Return code: 0; Memory used: 0.158GB
PID: 21548; 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_40/QC_hg38/H9_PRO-seq_40_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_plus_coverage.bed` (21554)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.662GB.
PID: 21554; Command: bedtools; Return code: 0; Memory used: 0.016GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_minus_coverage.bed` (21561)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.662GB.
PID: 21561; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron_sort.bed` (21568,21569,21570,21571)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB.
PID: 21568; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 21570; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 21569; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 21571; Command: bedtools; Return code: 0; Memory used: 0.077GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_plus_coverage.bed` (21574)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.662GB.
PID: 21574; Command: bedtools; Return code: 0; Memory used: 0.041GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_minus_coverage.bed` (21583)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.662GB.
PID: 21583; Command: bedtools; Return code: 0; Memory used: 0.022GB
### Plot cFRiF/FRiF (06-15 08:39:54) elapsed: 95.0 _TIME_
> `samtools view -@ 8 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_40 -z 3099922541 -n 3978050 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_plus_coverage.bed` (21601)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:38. Running peak memory: 3.662GB.
PID: 21601; Command: Rscript; Return code: 0; Memory used: 0.438GB
> `cFRiF` QC_hg38/H9_PRO-seq_40_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_40_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_40 -z 3099922541 -n 3978050 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_plus_coverage.bed` (21892)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:29. Running peak memory: 3.662GB.
PID: 21892; Command: Rscript; Return code: 0; Memory used: 0.438GB
> `FRiF` QC_hg38/H9_PRO-seq_40_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_40_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-15 08:41:01) elapsed: 67.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_exons_sort.bed` (21927,21928)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB.
PID: 21928; Command: bedtools; Return code: 0; Memory used: 0.086GB
PID: 21927; Command: grep; Return code: 0; Memory used: 0.004GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_introns_sort.bed` (21934,21935,21936)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB.
PID: 21934; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 21936; Command: bedtools; Return code: 0; Memory used: 0.003GB
PID: 21935; Command: bedtools; Return code: 0; Memory used: 0.033GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exons_coverage.bed` (21942)
Command completed. Elapsed time: 0:00:11. Running peak memory: 3.662GB.
PID: 21942; Command: bedtools; Return code: 0; Memory used: 0.008GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_coverage.bed` (21953)
Command completed. Elapsed time: 0:00:13. Running peak memory: 3.662GB.
PID: 21953; Command: bedtools; Return code: 0; Memory used: 0.019GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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]/7.2656885)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exons_rpkm.bed` (21965,21966,21967)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB.
PID: 21965; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 21967; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 21966; 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_40/QC_hg38/H9_PRO-seq_40_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]/7.2656885)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_rpkm.bed` (21970,21971,21972)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB.
PID: 21970; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 21972; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 21971; 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_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed` (21974,21975,21976)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 21974; Command: join; Return code: 0; Memory used: 0.001GB
PID: 21976; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 21975; 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_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed --annotate` (21983)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB.
PID: 21983; Command: Rscript; Return code: 0; Memory used: 0.295GB
> `mRNA contamination` QC_hg38/H9_PRO-seq_40_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_40_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed.gz`
> `pigz -f -p 8 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed` (22003)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB.
PID: 22003; Command: pigz; Return code: 0; Memory used: 0.002GB
### Produce bigWig files (06-15 08:41:43) elapsed: 42.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam` (22011)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.662GB.
PID: 22011; Command: samtools; Return code: 0; Memory used: 0.006GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/signal_hg38/H9_PRO-seq_40_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_smooth_body_0-mer.bw -p 5 --variable-step --tail-edge --scale 7265688.5` (22015)
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_40/aligned_hg38/H9_PRO-seq_40_plus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_40_plus_cuttrace_yc274ool'
Processing with 2 cores...
stdin is empty of data
Discarding 124 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', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr14_KI270724v1_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_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1']
Keeping 71 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', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_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_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 71 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_exact_body_0-mer.bw'
Merging 71 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:09:57. Running peak memory: 3.662GB.
PID: 22015; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.633GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam` (23614)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.662GB.
PID: 23614; Command: samtools; Return code: 0; Memory used: 0.005GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/signal_hg38/H9_PRO-seq_40_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_smooth_body_0-mer.bw -p 5 --variable-step --tail-edge --scale 7265688.5` (23618)
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_40/aligned_hg38/H9_PRO-seq_40_minus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_40_minus_cuttrace_hhgm_zea'
Processing with 2 cores...
stdin is empty of data
Discarding 123 chunk(s) of reads: ['chrM', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_KI270722v1_random', 'chr14_KI270723v1_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_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', 'chrUn_GL000214v1']
Keeping 72 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_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr14_GL000225v1_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_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_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 72 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_exact_body_0-mer.bw'
Merging 72 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:09:51. Running peak memory: 3.662GB.
PID: 23618; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.634GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 1:44:21
* Total elapsed time (all runs): 3:08:26
* Peak memory (this run): 3.6624 GB
* Pipeline completed time: 2020-06-15 09:01:38