### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_1 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --input2 /project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba25-34c0
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/
* Pipeline started at: (06-15 07:17:16) elapsed: 1.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE1.fastq.gz']`
* `input2`: `['/project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE2.fastq.gz']`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `12000`
* `new_start`: `False`
* `no_fifo`: `False`
* `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline`
* `paired_end`: `True`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `PRO`
* `recover`: `True`
* `sample_name`: `H9_PRO-seq_1`
* `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_DMSO_rep1_PE1.fastq.gz
Local input file: /project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE2.fastq.gz
> `File_mb` 2469.73 PEPPRO _RES_
> `Read_type` PAIRED PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-15 07:17:17) elapsed: 2.0 _TIME_
Number of input file sets: 2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R1.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R1.fastq.gz` (261655)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 261655; 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_1/raw/H9_PRO-seq_1_R1.fastq.gz'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R2.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R2.fastq.gz` (261657)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 261657; 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_1/raw/H9_PRO-seq_1_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_1/fastq/H9_PRO-seq_1_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2.fastq`
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1.fastq` (261662)
Command completed. Elapsed time: 0:02:40. Running peak memory: 0.002GB.
PID: 261662; Command: pigz; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2.fastq` (41970)
Command completed. Elapsed time: 0:01:34. Running peak memory: 0.002GB.
PID: 41970; Command: pigz; Return code: 0; Memory used: 0.002GB
> `Raw_reads` 97729860 PEPPRO _RES_
> `Fastq_reads` 97729860 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R2.fastq.gz']
### FASTQ processing: (06-15 07:23:33) elapsed: 376.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq`
> `(cutadapt -j 12 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/cutadapt/H9_PRO-seq_1_R1_cutadapt.txt` (233666)
Command completed. Elapsed time: 0:01:19. Running peak memory: 3.252GB.
PID: 233666; Command: cutadapt; Return code: 0; Memory used: 3.252GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq` (233763,233764)
Command completed. Elapsed time: 0:01:10. Running peak memory: 3.252GB.
PID: 233763; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 233764; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 30221343 PEPPRO _RES_
> `Trim_loss_rate` 69.08 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq` (234065)
Got SIGTERM. Failing gracefully... (06-15 12:57:44) elapsed: 20051.0 _TIME_
Child process 234065 (fastqc) terminated after 0 sec.
Setting dynamic recover file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/recover.lock.fastq__H9_PRO-seq_1_R1_processed.fastq
Setting dynamic recover file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/recover.lock.trimmed_fastqc
### Pipeline failed at: (06-15 12:57:44) elapsed: 0.0 _TIME_
Total time: 5:40:29
Failure reason: SIGTERM
Pipeline aborted.
### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_1 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --input2 /project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba25-12c0
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/
* Pipeline started at: (06-15 12:59:45) elapsed: 36.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE1.fastq.gz']`
* `input2`: `['/project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE2.fastq.gz']`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `12000`
* `new_start`: `False`
* `no_fifo`: `False`
* `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline`
* `paired_end`: `True`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `PRO`
* `recover`: `True`
* `sample_name`: `H9_PRO-seq_1`
* `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_DMSO_rep1_PE1.fastq.gz
Local input file: /project/shefflab/data//guertin/fastq/H9_DMSO_rep1_PE2.fastq.gz
> `File_mb` 2469.73 PEPPRO _RES_
> `Read_type` PAIRED PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-15 12:59:46) elapsed: 1.0 _TIME_
Number of input file sets: 2
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R1.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R1.fastq.gz'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R2.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R2.fastq.gz'
Found .fastq.gz file
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1.fastq`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/H9_PRO-seq_1_R2.fastq.gz']
### FASTQ processing: (06-15 12:59:46) elapsed: 0.0 _TIME_
> `cutadapt --version`
Found lock file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/lock.fastq__H9_PRO-seq_1_R1_processed.fastq
Overwriting target...
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq`
> `(cutadapt -j 12 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/cutadapt/H9_PRO-seq_1_R1_cutadapt.txt` (14926)
Command completed. Elapsed time: 0:00:59. Running peak memory: 3.258GB.
PID: 14926; Command: cutadapt; Return code: 0; Memory used: 3.258GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq` (15390,15391)
Command completed. Elapsed time: 0:00:33. Running peak memory: 3.258GB.
PID: 15390; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 15391; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 30221343 PEPPRO _RES_
> `Trim_loss_rate` 69.08 PEPPRO _RES_
Found lock file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/lock.trimmed_fastqc
Overwriting target...
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq` (15447)
Started analysis of H9_PRO-seq_1_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 20% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 25% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 35% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_1_R1_processed.fastq
Analysis complete for H9_PRO-seq_1_R1_processed.fastq
Command completed. Elapsed time: 0:00:57. Running peak memory: 3.258GB.
PID: 15447; Command: fastqc; Return code: 0; Memory used: 0.182GB
> `FastQC report r1` fastqc/H9_PRO-seq_1_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_1/fastq/H9_PRO-seq_1_R1_trimmed.fastq`
> `seqkit rmdup --threads 12 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_noadap.fastq` (15527)
[INFO][0m 3516802 duplicated records removed
Command completed. Elapsed time: 0:00:56. Running peak memory: 3.258GB.
PID: 15527; Command: seqkit; Return code: 0; Memory used: 2.002GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_trimmed.fastq` (15609,15610)
Command completed. Elapsed time: 0:00:24. Running peak memory: 3.258GB.
PID: 15609; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 15610; 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_1/cutadapt/H9_PRO-seq_1_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 34822522.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/cutadapt/H9_PRO-seq_1_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_1/cutadapt/H9_PRO-seq_1_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 17998987.0 PEPPRO _RES_
> `Duplicate_reads` 3516802.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 36.8342 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/processed_R1.flag` (15713)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.258GB.
PID: 15713; 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_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq`
> `(cutadapt -j 12 -m 10 -O 1 -a GATCGTCGGACTGTAGAACTCTGAAC /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/cutadapt/H9_PRO-seq_1_R2_cutadapt.txt` (15715)
Command completed. Elapsed time: 0:00:54. Running peak memory: 3.432GB.
PID: 15715; Command: cutadapt; Return code: 0; Memory used: 3.432GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq` (15801,15802)
Command completed. Elapsed time: 0:00:26. Running peak memory: 3.432GB.
PID: 15801; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 15802; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 60442686 PEPPRO _RES_
> `Trim_loss_rate` 38.15 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq` (16066)
Started analysis of H9_PRO-seq_1_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 20% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 25% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 35% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_1_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_1_R1_processed.fastq
Analysis complete for H9_PRO-seq_1_R1_processed.fastq
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f999e503631, pid=16066, tid=0x00007f9983bfb700
#
# JRE version: Java(TM) SE Runtime Environment (8.0_171-b11) (build 1.8.0_171-b11)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.171-b11 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V [libjvm.so+0x4b3631] CompileBroker::invoke_compiler_on_method(CompileTask*)+0x5a1
#
# Core dump written. Default location: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/core or core.16066
#
# An error report file with more information is saved as:
# /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/hs_err_pid16066.log
#
# If you would like to submit a bug report, please visit:
# http://bugreport.java.com/bugreport/crash.jsp
#
Command completed. Elapsed time: 0:00:58. Running peak memory: 3.432GB.
PID: 16066; Command: fastqc; Return code: -6; Memory used: 0.18GB
Subprocess returned nonzero result. Check above output for details
ERROR: Subprocess returned nonzero result, but pipeline is continuing because nofail=True
> `FastQC report r1` fastqc/H9_PRO-seq_1_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_1/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq` (16137)
Started analysis of H9_PRO-seq_1_R2_trimmed.fastq
Approx 5% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 10% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 15% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 20% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 25% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 30% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 35% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 40% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 45% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 50% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 55% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 60% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 65% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 70% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 75% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 80% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 85% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 90% complete for H9_PRO-seq_1_R2_trimmed.fastq
Approx 95% complete for H9_PRO-seq_1_R2_trimmed.fastq
Analysis complete for H9_PRO-seq_1_R2_trimmed.fastq
Command completed. Elapsed time: 0:00:54. Running peak memory: 3.432GB.
PID: 16137; Command: fastqc; Return code: 0; Memory used: 0.17GB
> `FastQC report r2` fastqc/H9_PRO-seq_1_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_1/cutadapt/H9_PRO-seq_1.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/cutadapt/H9_PRO-seq_1.histogram`
> `fastq_pair -t 87956874 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_noadap.fastq` (16204)
Left paired: 30692275 Right paired: 30692275
Left single: 173668 Right single: 1557501
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_noadap.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_noadap.fastq.single.fq
Command completed. Elapsed time: 0:02:42. Running peak memory: 6.12GB.
PID: 16204; Command: fastq_pair; Return code: 0; Memory used: 6.12GB
> `flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_noadap.fastq.paired.fq -o H9_PRO-seq_1 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/cutadapt` (16448)
Command completed. Elapsed time: 0:00:59. Running peak memory: 6.12GB.
PID: 16448; Command: flash; Return code: 0; Memory used: 0.094GB
### Plot adapter insertion distribution (06-15 13:10:55) elapsed: 669.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/cutadapt/H9_PRO-seq_1_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_1/cutadapt/H9_PRO-seq_1.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/cutadapt -u 8` (16944)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.12GB.
PID: 16944; Command: Rscript; Return code: 0; Memory used: 0.311GB
> `Adapter insertion distribution` cutadapt/H9_PRO-seq_1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_1_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_1/cutadapt/H9_PRO-seq_1.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 13:11:00) elapsed: 5.0 _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_1/cutadapt/H9_PRO-seq_1.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_1/cutadapt/H9_PRO-seq_1.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_1/cutadapt/H9_PRO-seq_1.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_1/cutadapt/H9_PRO-seq_1.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_1/cutadapt/H9_PRO-seq_1.hist`
> `Degradation_ratio` 0.8896 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed_dups.fastq`
> `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed_dups.fastq` (16973)
Command completed. Elapsed time: 0:00:21. Running peak memory: 6.12GB.
PID: 16973; 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_1/fastq/processed_R2.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/processed_R2.flag` (17341)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.12GB.
PID: 17341; 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_1/fastq/repaired.flag`
> `fastq_pair -t 87956874 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq` (17348)
Left paired: 30003416 Right paired: 30003416
Left single: 217927 Right single: 1602455
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq.single.fq
Command completed. Elapsed time: 0:02:32. Running peak memory: 6.178GB.
PID: 17348; Command: fastq_pair; Return code: 0; Memory used: 6.178GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq` (17984)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 17984; Command: mv; Return code: 0; Memory used: 0.002GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq` (17986)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 17986; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/repaired.flag` (17988)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 17988; 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_1/fastq/dups_repaired.flag`
> `fastq_pair -t 87956874 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed_dups.fastq` (17989)
Left paired: 26674489 Right paired: 26674489
Left single: 126830 Right single: 4931382
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed_dups.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed_dups.fastq.single.fq
Command completed. Elapsed time: 0:01:59. Running peak memory: 6.178GB.
PID: 17989; Command: fastq_pair; Return code: 0; Memory used: 6.154GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_trimmed.fastq` (19059)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 19059; Command: mv; Return code: 0; Memory used: 0.002GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed_dups.fastq` (19060)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 19060; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/dups_repaired.flag` (19063)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 19063; Command: touch; Return code: 0; Memory used: 0.0GB
### Prealignments (06-15 13:15:55) elapsed: 295.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-15 13:15:55) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/human_rDNA_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/human_rDNA_bt2` (19064)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 19064; Command: mkfifo; Return code: 0; Memory used: 0.0GB
File not added to cleanup: prealignments/human_rDNA_bt2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_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_1/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_R2.fq` (19065)
> `(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id H9_PRO-seq_1 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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'
30003416 reads; of these:
30003416 (100.00%) were unpaired; of these:
27299076 (90.99%) aligned 0 times
2704340 (9.01%) aligned exactly 1 time
0 (0.00%) aligned >1 times
9.01% overall alignment rate
> `Aligned_reads_human_rDNA` 5408680.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 8.95 PEPPRO _RES_
### Map to human_rDNA (06-15 13:19:19) elapsed: 204.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/human_rDNA_dups_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/human_rDNA_dups_bt2` (19503)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 19503; 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_1/prealignments/H9_PRO-seq_1_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_1/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_dups_R2.fq` (19504)
> `(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id H9_PRO-seq_1 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/fastq/H9_PRO-seq_1_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)`
not gzipping output
2704340 reads skipped
0 reads lost
File not added to cleanup: prealignments/human_rDNA_dups_bt2
### Map to genome (06-15 13:22:29) elapsed: 189.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_fail_qc_dups.bam
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort.bam`
> `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_1 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_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_1/aligned_hg38/tmp909od977 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp.bam` (20319,20320,20321)
2176982 reads skipped
0 reads lost
27299076 reads; of these:
27299076 (100.00%) were paired; of these:
9566070 (35.04%) aligned concordantly 0 times
14769056 (54.10%) aligned concordantly exactly 1 time
2963950 (10.86%) aligned concordantly >1 times
----
9566070 pairs aligned concordantly 0 times; of these:
2129010 (22.26%) aligned discordantly 1 time
----
7437060 pairs aligned 0 times concordantly or discordantly; of these:
14874120 mates make up the pairs; of these:
6258301 (42.08%) aligned 0 times
3282618 (22.07%) aligned exactly 1 time
5333201 (35.86%) aligned >1 times
88.54% overall alignment rate
[bam_sort_core] merging from 15 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:46:17. Running peak memory: 6.178GB.
PID: 20320; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 20319; Command: bowtie2; Return code: 0; Memory used: 3.802GB
PID: 20321; Command: samtools; Return code: 0; Memory used: 0.897GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort.bam` (24875)
Command completed. Elapsed time: 0:01:24. Running peak memory: 6.178GB.
PID: 24875; Command: samtools; Return code: 0; Memory used: 0.018GB
> `samtools depth -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 48339851 PEPPRO _RES_
> `QC_filtered_reads` 27585022 PEPPRO _RES_
> `Aligned_reads` 20754829.0 PEPPRO _RES_
> `Alignment_rate` 34.34 PEPPRO _RES_
> `Total_efficiency` 21.24 PEPPRO _RES_
> `Read_depth` 3.26 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort_dups.bam`
> `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_1 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_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_1/aligned_hg38/tmp909od977 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp_dups.bam` (26249,26255,26256)
24497507 reads; of these:
24497507 (100.00%) were paired; of these:
8334941 (34.02%) aligned concordantly 0 times
13482466 (55.04%) aligned concordantly exactly 1 time
2680100 (10.94%) aligned concordantly >1 times
----
8334941 pairs aligned concordantly 0 times; of these:
1950931 (23.41%) aligned discordantly 1 time
----
6384010 pairs aligned 0 times concordantly or discordantly; of these:
12768020 mates make up the pairs; of these:
5376104 (42.11%) aligned 0 times
3000379 (23.50%) aligned exactly 1 time
4391537 (34.39%) aligned >1 times
89.03% overall alignment rate
[bam_sort_core] merging from 14 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:41:14. Running peak memory: 6.178GB.
PID: 26249; Command: bowtie2; Return code: 0; Memory used: 3.767GB
PID: 26255; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 26256; Command: samtools; Return code: 0; Memory used: 0.897GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort_dups.bam` (30214)
Command completed. Elapsed time: 0:01:17. Running peak memory: 6.178GB.
PID: 30214; Command: samtools; Return code: 0; Memory used: 0.018GB
### Compress all unmapped read files (06-15 15:05:53) elapsed: 6204.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_R2.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_R2.fq` (30427)
Command completed. Elapsed time: 0:00:21. Running peak memory: 6.178GB.
PID: 30427; Command: pigz; Return code: 0; Memory used: 0.009GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_R1.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/prealignments/H9_PRO-seq_1_human_rDNA_unmap_R1.fq` (30459)
Command completed. Elapsed time: 0:00:25. Running peak memory: 6.178GB.
PID: 30459; Command: pigz; Return code: 0; Memory used: 0.009GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp.bam` (30497)
Command completed. Elapsed time: 0:00:38. Running peak memory: 6.178GB.
PID: 30497; Command: samtools; Return code: 0; Memory used: 0.01GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 674956 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort.bam` (30537)
Command completed. Elapsed time: 0:00:29. Running peak memory: 6.178GB.
PID: 30537; Command: samtools; Return code: 0; Memory used: 0.012GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_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_1/aligned_hg38/chr_sizes.bed` (30565,30566,30567,30568)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 30565; Command: samtools; Return code: 0; Memory used: 0.003GB
PID: 30567; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 30566; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 30568; Command: grep; Return code: 0; Memory used: 0.003GB
> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_noMT.bam` (30570)
Command completed. Elapsed time: 0:00:41. Running peak memory: 6.178GB.
PID: 30570; Command: samtools; Return code: 0; Memory used: 0.019GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort.bam` (30622)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 30622; Command: mv; Return code: 0; Memory used: 0.002GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort.bam` (30623)
Command completed. Elapsed time: 0:00:29. Running peak memory: 6.178GB.
PID: 30623; Command: samtools; Return code: 0; Memory used: 0.011GB
### Split BAM file (06-15 15:08:57) elapsed: 184.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam` (30649,30650)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:46. Running peak memory: 6.178GB.
PID: 30649; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 30650; Command: samtools; Return code: 0; Memory used: 5.83GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE2.bam` (31033,31034)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:27. Running peak memory: 6.178GB.
PID: 31034; Command: samtools; Return code: 0; Memory used: 4.57GB
PID: 31033; Command: samtools; Return code: 0; Memory used: 0.004GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_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_1/aligned_hg38/H9_PRO-seq_1_temp_dups.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp_dups.bam` (31393)
Command completed. Elapsed time: 0:00:33. Running peak memory: 6.178GB.
PID: 31393; Command: samtools; Return code: 0; Memory used: 0.01GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_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_1/aligned_hg38/H9_PRO-seq_1_sort_dups.bam`
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort_dups.bam.bai
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_dups_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_dups_PE1.bam` (31436,31437)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:43. Running peak memory: 6.178GB.
PID: 31436; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 31437; Command: samtools; Return code: 0; Memory used: 5.399GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_dups_PE2.bam` (31655,31656)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:22. Running peak memory: 6.178GB.
PID: 31656; Command: samtools; Return code: 0; Memory used: 4.278GB
PID: 31655; Command: samtools; Return code: 0; Memory used: 0.004GB
### Calculate library complexity (06-15 15:20:47) elapsed: 710.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_preseq_out.txt`
> `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_dups_PE1.bam` (32034)
BAM_INPUT
TOTAL READS = 20330230
COUNTS_SUM = 20330230
DISTINCT READS = 1.66542e+07
DISTINCT COUNTS = 262
MAX COUNT = 16193
COUNTS OF 1 = 1.47277e+07
OBSERVED COUNTS (16194)
1 14727710
2 1349104
3 301309
4 112637
5 55354
6 31165
7 18956
8 12770
9 8912
10 6479
11 4906
12 3639
13 2910
14 2335
15 1909
16 1594
17 1295
18 1055
19 904
20 791
21 668
22 611
23 529
24 477
25 427
26 388
27 364
28 323
29 242
30 234
31 263
32 232
33 207
34 182
35 165
36 158
37 167
38 119
39 133
40 114
41 111
42 122
43 105
44 82
45 73
46 82
47 75
48 75
49 76
50 60
51 49
52 59
53 63
54 55
55 46
56 48
57 54
58 37
59 41
60 42
61 47
62 48
63 35
64 35
65 32
66 27
67 30
68 32
69 27
70 18
71 21
72 23
73 16
74 16
75 21
76 17
77 15
78 13
79 24
80 11
81 16
82 21
83 21
84 11
85 11
86 10
87 23
88 12
89 16
90 16
91 11
92 12
93 10
94 8
95 9
96 12
97 16
98 6
99 14
100 3
101 5
102 7
103 9
104 5
105 11
106 10
107 7
108 5
109 7
110 7
111 7
112 4
113 7
114 3
115 4
116 11
117 9
118 4
119 5
122 7
123 3
124 3
125 8
126 3
127 4
128 4
129 3
130 3
131 7
132 6
133 4
134 4
135 7
136 7
137 2
138 5
139 4
140 3
141 1
142 4
143 4
144 2
145 3
146 4
147 5
148 2
149 4
150 1
151 1
152 1
154 1
155 5
156 3
158 1
161 1
162 3
163 2
164 1
165 3
166 3
167 1
169 1
170 2
171 1
172 1
173 2
174 1
175 1
176 3
178 2
179 4
181 1
182 1
183 1
184 1
186 1
187 2
188 1
190 1
192 2
193 1
196 1
198 1
199 1
200 1
202 1
203 2
204 2
205 1
206 1
207 1
208 1
209 1
212 1
214 1
216 3
220 1
221 1
222 1
223 1
224 2
227 1
228 1
232 1
233 1
235 1
237 2
241 1
249 1
251 1
253 1
254 1
255 1
256 1
257 1
258 2
262 1
264 1
266 1
268 1
269 1
275 1
277 1
280 1
296 1
299 1
303 1
306 1
313 1
315 1
317 2
325 1
345 1
348 1
406 1
412 1
430 1
433 1
436 1
437 1
493 1
494 1
540 1
547 1
606 2
611 1
612 1
734 1
787 1
789 1
848 1
927 1
943 1
1376 1
1390 1
1414 1
2008 1
4768 1
5683 1
6998 1
14724 1
16193 1
sample size: 1000000
sample size: 2000000
sample size: 3000000
sample size: 4000000
sample size: 5000000
sample size: 6000000
sample size: 7000000
sample size: 8000000
sample size: 9000000
sample size: 10000000
sample size: 11000000
sample size: 12000000
sample size: 13000000
sample size: 14000000
sample size: 15000000
sample size: 16000000
sample size: 17000000
sample size: 18000000
sample size: 19000000
sample size: 20000000
Command completed. Elapsed time: 0:01:41. Running peak memory: 6.178GB.
PID: 32034; 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_1/QC_hg38/H9_PRO-seq_1_preseq_yield.txt`
> `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_dups_PE1.bam` (32142)
BAM_INPUT
TOTAL READS = 20330230
DISTINCT READS = 1.66542e+07
DISTINCT COUNTS = 262
MAX COUNT = 16193
COUNTS OF 1 = 1.47277e+07
MAX TERMS = 100
OBSERVED COUNTS (16194)
1 14727710
2 1349104
3 301309
4 112637
5 55354
6 31165
7 18956
8 12770
9 8912
10 6479
11 4906
12 3639
13 2910
14 2335
15 1909
16 1594
17 1295
18 1055
19 904
20 791
21 668
22 611
23 529
24 477
25 427
26 388
27 364
28 323
29 242
30 234
31 263
32 232
33 207
34 182
35 165
36 158
37 167
38 119
39 133
40 114
41 111
42 122
43 105
44 82
45 73
46 82
47 75
48 75
49 76
50 60
51 49
52 59
53 63
54 55
55 46
56 48
57 54
58 37
59 41
60 42
61 47
62 48
63 35
64 35
65 32
66 27
67 30
68 32
69 27
70 18
71 21
72 23
73 16
74 16
75 21
76 17
77 15
78 13
79 24
80 11
81 16
82 21
83 21
84 11
85 11
86 10
87 23
88 12
89 16
90 16
91 11
92 12
93 10
94 8
95 9
96 12
97 16
98 6
99 14
100 3
101 5
102 7
103 9
104 5
105 11
106 10
107 7
108 5
109 7
110 7
111 7
112 4
113 7
114 3
115 4
116 11
117 9
118 4
119 5
122 7
123 3
124 3
125 8
126 3
127 4
128 4
129 3
130 3
131 7
132 6
133 4
134 4
135 7
136 7
137 2
138 5
139 4
140 3
141 1
142 4
143 4
144 2
145 3
146 4
147 5
148 2
149 4
150 1
151 1
152 1
154 1
155 5
156 3
158 1
161 1
162 3
163 2
164 1
165 3
166 3
167 1
169 1
170 2
171 1
172 1
173 2
174 1
175 1
176 3
178 2
179 4
181 1
182 1
183 1
184 1
186 1
187 2
188 1
190 1
192 2
193 1
196 1
198 1
199 1
200 1
202 1
203 2
204 2
205 1
206 1
207 1
208 1
209 1
212 1
214 1
216 3
220 1
221 1
222 1
223 1
224 2
227 1
228 1
232 1
233 1
235 1
237 2
241 1
249 1
251 1
253 1
254 1
255 1
256 1
257 1
258 2
262 1
264 1
266 1
268 1
269 1
275 1
277 1
280 1
296 1
299 1
303 1
306 1
313 1
315 1
317 2
325 1
345 1
348 1
406 1
412 1
430 1
433 1
436 1
437 1
493 1
494 1
540 1
547 1
606 2
611 1
612 1
734 1
787 1
789 1
848 1
927 1
943 1
1376 1
1390 1
1414 1
2008 1
4768 1
5683 1
6998 1
14724 1
16193 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
.................................................................................._......._...........
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]
Command completed. Elapsed time: 0:01:47. Running peak memory: 6.178GB.
PID: 32142; 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_1/QC_hg38/H9_PRO-seq_1_preseq_counts.txt`
> `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_preseq_counts.txt` (32237)
Command completed. Elapsed time: 0:00:29. Running peak memory: 6.178GB.
PID: 32237; 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_1/QC_hg38/H9_PRO-seq_1_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_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_1/QC_hg38/H9_PRO-seq_1_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_preseq_plot` (32272)
Processing H9_PRO-seq_1
INFO: Found real counts for H9_PRO-seq_1 - Total (M): 21.966708 Unique (M): 20.33023
Library complexity plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 6.178GB.
PID: 32272; Command: Rscript; Return code: 0; Memory used: 0.211GB
> `Library complexity` QC_hg38/H9_PRO-seq_1_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_1_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_1/QC_hg38/H9_PRO-seq_1_preseq_yield.txt | awk '{print $2}'`
> `Frac_exp_unique_at_10M` 0.8774 PEPPRO _RES_
### Calculate NRF, PBC1, and PBC2 (06-15 15:24:50) elapsed: 243.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam` (32292)
Command completed. Elapsed time: 0:00:18. Running peak memory: 6.178GB.
PID: 32292; Command: samtools; Return code: 0; Memory used: 0.014GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_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_1/aligned_hg38/H9_PRO-seq_1_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_bamQC.tsv` (32424)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/tmp_H9_PRO-seq_1_PE1_b_xgcpnk'
Processing with 12 cores...
Discarding 96 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270720v1_random', 'chr14_KI270724v1_random', 'chr22_KI270735v1_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_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270590v1', '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_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_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1']
Keeping 99 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270515v1', 'chrUn_KI270539v1', 'chrUn_KI270587v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270584v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Command completed. Elapsed time: 0:00:24. Running peak memory: 6.178GB.
PID: 32424; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.899GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_bamQC.tsv`
> `NRF` 1.0 PEPPRO _RES_
> `PBC1` 10983354.0 PEPPRO _RES_
> `PBC2` 10983354.0 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_unmap.bam`
> `samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_unmap.bam` (32480)
Command completed. Elapsed time: 0:00:09. Running peak memory: 6.178GB.
PID: 32480; Command: samtools; Return code: 0; Memory used: 0.009GB
> `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_temp.bam`
> `Unmapped_reads` 6258301 PEPPRO _RES_
### Split BAM by strand (06-15 15:25:48) elapsed: 58.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam` (32525)
Command completed. Elapsed time: 0:01:10. Running peak memory: 6.178GB.
PID: 32525; 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_1/aligned_hg38/H9_PRO-seq_1_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam` (32589)
Command completed. Elapsed time: 0:01:08. Running peak memory: 6.178GB.
PID: 32589; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-15 15:28:07) elapsed: 139.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (32652)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 32652; 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_1/QC_hg38/H9_PRO-seq_1_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_1/aligned_hg38/H9_PRO-seq_1_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_plus_TssEnrichment.txt` (32653)
Command completed. Elapsed time: 0:00:07. Running peak memory: 6.178GB.
PID: 32653; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.793GB
> `TSS_coding_score` 26.7 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_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_1/aligned_hg38/H9_PRO-seq_1_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_minus_TssEnrichment.txt` (32686)
Command completed. Elapsed time: 0:00:06. Running peak memory: 6.178GB.
PID: 32686; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.925GB
> `TSS_non-coding_score` 10.1 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_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_1/QC_hg38/H9_PRO-seq_1_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_minus_TssEnrichment.txt` (32721)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_minus_TssEnrichment.txt
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
TSS enrichment plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 6.178GB.
PID: 32721; Command: Rscript; Return code: 0; Memory used: 0.317GB
> `TSS enrichment` QC_hg38/H9_PRO-seq_1_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_1_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_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_1/QC_hg38/chr_order.txt` (32742,32743,32744,32745)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 32742; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 32744; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 32743; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 32745; 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_1/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_keep.txt` (32747)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 32747; Command: cut; Return code: 0; Memory used: 0.002GB
### Calculate Pause Index (PI) (06-15 15:28:26) elapsed: 19.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_ensembl_tss.bed` (32750,32751)
Command completed. Elapsed time: 0:00:02. Running peak memory: 6.178GB.
PID: 32750; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 32751; Command: bedtools; Return code: 0; Memory used: 0.046GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_ensembl_gene_body.bed` (32755,32756)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 32755; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 32756; 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_1/QC_hg38/H9_PRO-seq_1_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/H9_PRO-seq_1_TSS_density.bed` (32758,32759,32760,32761)
Command completed. Elapsed time: 0:00:27. Running peak memory: 6.178GB.
PID: 32759; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 32761; Command: sort; Return code: 0; Memory used: 0.002GB
PID: 32758; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 32760; Command: sort; Return code: 0; Memory used: 0.004GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_gene_body_density.bed` (32785,32786,32787)
Command completed. Elapsed time: 0:00:31. Running peak memory: 6.178GB.
PID: 32786; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 32785; Command: bedtools; Return code: 0; Memory used: 0.063GB
PID: 32787; Command: sort; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_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_1/QC_hg38/H9_PRO-seq_1_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_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_1/QC_hg38/tmp6bum7qxi` (32822,32823,32824)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 32822; Command: join; Return code: 0; Memory used: 0.001GB
PID: 32824; Command: env; Return code: 0; Memory used: 0.004GB
PID: 32823; 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_1/QC_hg38/tmp6bum7qxi | 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_1/QC_hg38/H9_PRO-seq_1_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.0210697) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/tmp6bum7qxi > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_pause_index.bed` (32831)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 32831; 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_1/QC_hg38/H9_PRO-seq_1_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` 26.45 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_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_1/QC_hg38/H9_PRO-seq_1_pause_index.bed` (32836)
Pause index plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.178GB.
PID: 32836; Command: Rscript; Return code: 0; Memory used: 0.317GB
> `Pause index` QC_hg38/H9_PRO-seq_1_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_1_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_pause_index.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_pause_index.bed` (32857)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 32857; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-15 15:29:32) elapsed: 65.0 _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_1/aligned_hg38/H9_PRO-seq_1_plus.bam`
20754829.0 7959339
> `Plus_FRiP` 0.38 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_1/aligned_hg38/H9_PRO-seq_1_minus.bam`
20754829.0 7448642
> `Minus_FRiP` 0.36 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_gene_sort.bed` (33122,33123)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 33122; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 33123; Command: bedtools; Return code: 0; Memory used: 0.006GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_gene_coverage.bed` (33126)
Command completed. Elapsed time: 0:00:31. Running peak memory: 6.178GB.
PID: 33126; Command: bedtools; Return code: 0; Memory used: 0.069GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/raw/hg38_annotations.bed.gz` (33158)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 33158; Command: ln; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/hg38_annotations.bed` (33159)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 33159; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 15:30:43) elapsed: 71.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/raw/hg38_annotations.bed` (33168)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 33168; 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_1/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Enhancer_sort.bed` (33170,33171,33172,33173)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 33170; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 33171; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 33173; Command: bedtools; Return code: 0; Memory used: 0.044GB
PID: 33172; 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_1/QC_hg38/H9_PRO-seq_1_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Enhancer_plus_coverage.bed` (33175)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.178GB.
PID: 33175; 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_1/QC_hg38/H9_PRO-seq_1_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Enhancer_minus_coverage.bed` (33193)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.178GB.
PID: 33193; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter_sort.bed` (33209,33210,33211,33212)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 33209; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 33210; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 33212; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 33211; 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_1/QC_hg38/H9_PRO-seq_1_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_plus_coverage.bed` (33214)
Command completed. Elapsed time: 0:00:14. Running peak memory: 6.178GB.
PID: 33214; Command: bedtools; Return code: 0; Memory used: 0.024GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_minus_coverage.bed` (33234)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.178GB.
PID: 33234; Command: bedtools; Return code: 0; Memory used: 0.017GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter_Flanking_Region"` (33251)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 33251; 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_1/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter_Flanking_Region_sort.bed` (33252,33253,33254,33255)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 33252; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 33254; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 33253; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 33255; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_Flanking_Region_plus_coverage.bed` (33257)
Command completed. Elapsed time: 0:00:14. Running peak memory: 6.178GB.
PID: 33257; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_Flanking_Region_minus_coverage.bed` (33271)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.178GB.
PID: 33271; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/5_UTR"` (33286)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 33286; 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_1/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/5_UTR_sort.bed` (33287,33288,33289,33290)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 33287; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 33288; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 33290; Command: bedtools; Return code: 0; Memory used: 0.03GB
PID: 33289; 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_1/QC_hg38/H9_PRO-seq_1_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_5_UTR_plus_coverage.bed` (33292)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.178GB.
PID: 33292; 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_1/QC_hg38/H9_PRO-seq_1_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_5_UTR_minus_coverage.bed` (33309)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.178GB.
PID: 33309; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/3_UTR"` (33326)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 33326; 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_1/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/3_UTR_sort.bed` (33327,33328,33329,33330)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 33327; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 33328; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 33330; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 33329; 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_1/QC_hg38/H9_PRO-seq_1_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_3_UTR_plus_coverage.bed` (33333)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.178GB.
PID: 33333; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_3_UTR_minus_coverage.bed` (33349)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.178GB.
PID: 33349; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Exon_sort.bed` (33364,33365,33366,33367)
Command completed. Elapsed time: 0:00:03. Running peak memory: 6.178GB.
PID: 33364; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 33365; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 33367; Command: bedtools; Return code: 0; Memory used: 0.158GB
PID: 33366; 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_1/QC_hg38/H9_PRO-seq_1_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Exon_plus_coverage.bed` (33373)
Command completed. Elapsed time: 0:00:15. Running peak memory: 6.178GB.
PID: 33373; Command: bedtools; Return code: 0; Memory used: 0.025GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Exon_minus_coverage.bed` (33390)
Command completed. Elapsed time: 0:00:14. Running peak memory: 6.178GB.
PID: 33390; Command: bedtools; Return code: 0; Memory used: 0.022GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Intron_sort.bed` (33408,33409,33410,33411)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 33408; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 33410; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 33409; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 33411; 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_1/QC_hg38/H9_PRO-seq_1_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Intron_plus_coverage.bed` (33415)
Command completed. Elapsed time: 0:00:16. Running peak memory: 6.178GB.
PID: 33415; Command: bedtools; Return code: 0; Memory used: 0.056GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Intron_minus_coverage.bed` (33468)
Command completed. Elapsed time: 0:00:15. Running peak memory: 6.178GB.
PID: 33468; Command: bedtools; Return code: 0; Memory used: 0.039GB
### Plot cFRiF/FRiF (06-15 15:34:04) elapsed: 201.0 _TIME_
> `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_1 -z 3099922541 -n 11202246 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Intron_plus_coverage.bed` (33502)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:33. Running peak memory: 6.178GB.
PID: 33502; Command: Rscript; Return code: 0; Memory used: 0.501GB
> `cFRiF` QC_hg38/H9_PRO-seq_1_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_1_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_1 -z 3099922541 -n 11202246 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_Intron_plus_coverage.bed` (33548)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:24. Running peak memory: 6.178GB.
PID: 33548; Command: Rscript; Return code: 0; Memory used: 0.501GB
> `FRiF` QC_hg38/H9_PRO-seq_1_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_1_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-15 15:35:02) elapsed: 58.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_exons_sort.bed` (33698,33699)
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.178GB.
PID: 33698; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 33699; Command: bedtools; Return code: 0; Memory used: 0.093GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/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_1/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_introns_sort.bed` (33705,33706,33707)
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.178GB.
PID: 33705; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 33707; Command: bedtools; Return code: 0; Memory used: 0.005GB
PID: 33706; 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_1/QC_hg38/H9_PRO-seq_1_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_exons_coverage.bed` (33719)
Command completed. Elapsed time: 0:00:26. Running peak memory: 6.178GB.
PID: 33719; Command: bedtools; Return code: 0; Memory used: 0.013GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_introns_coverage.bed` (33747)
Command completed. Elapsed time: 0:00:29. Running peak memory: 6.178GB.
PID: 33747; 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_1/QC_hg38/H9_PRO-seq_1_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]/20.754829)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_exons_rpkm.bed` (33772,33773,33774)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 33772; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 33774; Command: sort; Return code: 0; Memory used: 0.003GB
PID: 33773; 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_1/QC_hg38/H9_PRO-seq_1_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]/20.754829)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_introns_rpkm.bed` (33776,33777,33778)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.178GB.
PID: 33776; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 33778; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 33777; 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_1/QC_hg38/H9_PRO-seq_1_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_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_1/QC_hg38/H9_PRO-seq_1_exon_intron_ratios.bed` (33781,33782,33783)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 33781; Command: join; Return code: 0; Memory used: 0.001GB
PID: 33783; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 33782; 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_1/QC_hg38/H9_PRO-seq_1_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` 1.23 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_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_1/QC_hg38/H9_PRO-seq_1_exon_intron_ratios.bed --annotate` (33789)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.178GB.
PID: 33789; Command: Rscript; Return code: 0; Memory used: 0.317GB
> `mRNA contamination` QC_hg38/H9_PRO-seq_1_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_1_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_exon_intron_ratios.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/QC_hg38/H9_PRO-seq_1_exon_intron_ratios.bed` (33810)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.178GB.
PID: 33810; Command: pigz; Return code: 0; Memory used: 0.003GB
### Produce bigWig files (06-15 15:36:13) elapsed: 71.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_plus.bam` (33818)
Command completed. Elapsed time: 0:00:10. Running peak memory: 6.178GB.
PID: 33818; Command: samtools; Return code: 0; Memory used: 0.008GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_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_1/signal_hg38/H9_PRO-seq_1_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 20754829.0` (33829)
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_1/aligned_hg38/H9_PRO-seq_1_plus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_1_plus_cuttrace_exvi9dtb'
Processing with 4 cores...
stdin is empty of data
Discarding 115 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270720v1_random', 'chr14_KI270724v1_random', 'chr22_KI270735v1_random', 'chr22_KI270737v1_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_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_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', '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_GL000213v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1']
Keeping 80 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270438v1', 'chrUn_KI270515v1', 'chrUn_KI270539v1', 'chrUn_KI270587v1', 'chrUn_KI270589v1', 'chrUn_KI270584v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 80 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_plus_exact_body_0-mer.bw'
Merging 80 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:06:18. Running peak memory: 6.178GB.
PID: 33829; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.346GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_minus.bam` (35275)
Command completed. Elapsed time: 0:00:08. Running peak memory: 6.178GB.
PID: 35275; Command: samtools; Return code: 0; Memory used: 0.009GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/aligned_hg38/H9_PRO-seq_1_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_1/signal_hg38/H9_PRO-seq_1_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 20754829.0` (35283)
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_1/aligned_hg38/H9_PRO-seq_1_minus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_1_minus_cuttrace_j2gcnfml'
Processing with 4 cores...
stdin is empty of data
stdin is empty of data
Discarding 109 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_KI270722v1_random', 'chr14_KI270724v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270735v1_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_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', '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_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_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1']
Keeping 86 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270708v1_random', 'chr1_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', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270521v1', '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_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 86 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_minus_exact_body_0-mer.bw'
Merging 86 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_1/signal_hg38/H9_PRO-seq_1_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:07:12. Running peak memory: 6.178GB.
PID: 35283; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.763GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 2:50:51
* Total elapsed time (all runs): 5:20:58
* Peak memory (this run): 6.178 GB
* Pipeline completed time: 2020-06-15 15:50:01