### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_90 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_90pct_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --input2 /project/shefflab/data//guertin/fastq/H9_PRO-seq_90pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba26-35c0
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/
* Pipeline started at: (06-15 07:17:27) elapsed: 2.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_90pct_PE1.fastq.gz']`
* `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_90pct_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_90`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `PAIRED`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `8`
* `verbosity`: `None`
----------------------------------------
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_90pct_PE1.fastq.gz
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_90pct_PE2.fastq.gz
> `File_mb` 2146.02 PEPPRO _RES_
> `Read_type` PAIRED PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-15 07:17:28) elapsed: 1.0 _TIME_
Number of input file sets: 2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/H9_PRO-seq_90_R1.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_90pct_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/H9_PRO-seq_90_R1.fastq.gz` (217612)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 217612; 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_90/raw/H9_PRO-seq_90_R1.fastq.gz'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/H9_PRO-seq_90_R2.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_90pct_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/H9_PRO-seq_90_R2.fastq.gz` (217614)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.
PID: 217614; 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_90/raw/H9_PRO-seq_90_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_90/fastq/H9_PRO-seq_90_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2.fastq`
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/H9_PRO-seq_90_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1.fastq` (217617)
Command completed. Elapsed time: 0:02:50. Running peak memory: 0.002GB.
PID: 217617; 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_90/raw/H9_PRO-seq_90_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2.fastq` (350867)
Command completed. Elapsed time: 0:02:27. Running peak memory: 0.002GB.
PID: 350867; Command: pigz; Return code: 0; Memory used: 0.002GB
> `Raw_reads` 104146252 PEPPRO _RES_
> `Fastq_reads` 104146252 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/H9_PRO-seq_90_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/H9_PRO-seq_90_R2.fastq.gz']
### FASTQ processing: (06-15 07:26:06) elapsed: 518.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_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_90/fastq/H9_PRO-seq_90_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/cutadapt/H9_PRO-seq_90_R1_cutadapt.txt` (332572)
Command completed. Elapsed time: 0:02:48. Running peak memory: 3.094GB.
PID: 332572; Command: cutadapt; Return code: 0; Memory used: 3.094GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq` (332770,332771)
Command completed. Elapsed time: 0:00:52. Running peak memory: 3.094GB.
PID: 332770; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 332771; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 25498419 PEPPRO _RES_
> `Trim_loss_rate` 75.52 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq` (332870)
Started analysis of H9_PRO-seq_90_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 20% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 25% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 35% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_90_R1_processed.fastq
Analysis complete for H9_PRO-seq_90_R1_processed.fastq
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007fba053fb8a9, pid=332870, tid=0x00007fb9e9eec700
#
# 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+0x6e08a9] jni_ReleasePrimitiveArrayCritical+0x69
#
# Core dump written. Default location: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/core or core.332870
#
# An error report file with more information is saved as:
# /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/hs_err_pid332870.log
#
# If you would like to submit a bug report, please visit:
# http://bugreport.java.com/bugreport/crash.jsp
#
Command completed. Elapsed time: 0:00:56. Running peak memory: 3.094GB.
PID: 332870; Command: fastqc; Return code: -6; Memory used: 0.178GB
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_90_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_90/fastq/H9_PRO-seq_90_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_90/fastq/H9_PRO-seq_90_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_noadap.fastq` (333200)
[INFO][0m 2562794 duplicated records removed
Command completed. Elapsed time: 0:01:02. Running peak memory: 3.094GB.
PID: 333200; Command: seqkit; Return code: 0; Memory used: 2.048GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_trimmed.fastq` (333284,333285)
Command completed. Elapsed time: 0:00:50. Running peak memory: 3.094GB.
PID: 333284; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 333285; 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_90/cutadapt/H9_PRO-seq_90_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 41262698.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/cutadapt/H9_PRO-seq_90_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_90/cutadapt/H9_PRO-seq_90_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 25749458.0 PEPPRO _RES_
> `Duplicate_reads` 2562794.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 49.4487 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/processed_R1.flag` (333542)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.094GB.
PID: 333542; 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_90/fastq/H9_PRO-seq_90_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_90/fastq/H9_PRO-seq_90_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/cutadapt/H9_PRO-seq_90_R2_cutadapt.txt` (333544)
Command completed. Elapsed time: 0:02:09. Running peak memory: 3.381GB.
PID: 333544; Command: cutadapt; Return code: 0; Memory used: 3.381GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed.fastq` (333910,333911)
Command completed. Elapsed time: 0:00:33. Running peak memory: 3.381GB.
PID: 333910; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 333911; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 50996838 PEPPRO _RES_
> `Trim_loss_rate` 51.03 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq` (334000)
Started analysis of H9_PRO-seq_90_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 20% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 25% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 35% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_90_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_90_R1_processed.fastq
Analysis complete for H9_PRO-seq_90_R1_processed.fastq
Command completed. Elapsed time: 0:00:56. Running peak memory: 3.381GB.
PID: 334000; Command: fastqc; Return code: 0; Memory used: 0.179GB
> `FastQC report r1` fastqc/H9_PRO-seq_90_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_90/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed.fastq` (334070)
Started analysis of H9_PRO-seq_90_R2_trimmed.fastq
Approx 5% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 10% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 15% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 20% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 25% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 30% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 35% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 40% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 45% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 50% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 55% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 60% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 65% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 70% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 75% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 80% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 85% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 90% complete for H9_PRO-seq_90_R2_trimmed.fastq
Approx 95% complete for H9_PRO-seq_90_R2_trimmed.fastq
Analysis complete for H9_PRO-seq_90_R2_trimmed.fastq
Command completed. Elapsed time: 0:01:05. Running peak memory: 3.381GB.
PID: 334070; Command: fastqc; Return code: 0; Memory used: 0.166GB
> `FastQC report r2` fastqc/H9_PRO-seq_90_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_90/cutadapt/H9_PRO-seq_90.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/cutadapt/H9_PRO-seq_90.histogram`
> `fastq_pair -t 93731626 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_noadap.fastq` (334203)
Left paired: 26141450 Right paired: 26141450
Left single: 182218 Right single: 2409759
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_noadap.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_noadap.fastq.single.fq
Command completed. Elapsed time: 0:03:26. Running peak memory: 5.91GB.
PID: 334203; Command: fastq_pair; Return code: 0; Memory used: 5.91GB
> `flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_noadap.fastq.paired.fq -o H9_PRO-seq_90 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/cutadapt` (334807)
Command completed. Elapsed time: 0:01:24. Running peak memory: 5.91GB.
PID: 334807; Command: flash; Return code: 0; Memory used: 0.126GB
### Plot adapter insertion distribution (06-15 07:44:33) elapsed: 1107.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/cutadapt/H9_PRO-seq_90_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_90/cutadapt/H9_PRO-seq_90.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/cutadapt -u 8` (335026)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.91GB.
PID: 335026; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `Adapter insertion distribution` cutadapt/H9_PRO-seq_90_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_90_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_90/cutadapt/H9_PRO-seq_90.hist | awk 'BEGIN{max= 0; max_len=0; len=0}{if ($2>0+max) {max=$2; len=$1}; max_len=$1} END{print len-8}'`
> `Peak_adapter_insertion_size` 20 PEPPRO _RES_
Missing stat 'Degradation_ratio'
### Calculating degradation ratio (06-15 07:44:38) 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_90/cutadapt/H9_PRO-seq_90.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_90/cutadapt/H9_PRO-seq_90.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_90/cutadapt/H9_PRO-seq_90.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_90/cutadapt/H9_PRO-seq_90.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_90/cutadapt/H9_PRO-seq_90.hist`
> `Degradation_ratio` 1.0318 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed_dups.fastq`
> `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed_dups.fastq` (335056)
Command completed. Elapsed time: 0:00:32. Running peak memory: 5.91GB.
PID: 335056; 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_90/fastq/processed_R2.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/processed_R2.flag` (335273)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 335273; 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_90/fastq/repaired.flag`
> `fastq_pair -t 93731626 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed.fastq` (335274)
Left paired: 25297086 Right paired: 25297086
Left single: 201333 Right single: 2474476
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed.fastq.single.fq
Command completed. Elapsed time: 0:02:55. Running peak memory: 5.91GB.
PID: 335274; Command: fastq_pair; Return code: 0; Memory used: 5.758GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq` (335620)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 335620; Command: mv; Return code: 0; Memory used: 0.001GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed.fastq` (335621)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 335621; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/repaired.flag` (335623)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 335623; 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_90/fastq/dups_repaired.flag`
> `fastq_pair -t 93731626 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed_dups.fastq` (335624)
Left paired: 22929753 Right paired: 22929753
Left single: 147931 Right single: 4841809
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed_dups.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed_dups.fastq.single.fq
Command completed. Elapsed time: 0:02:19. Running peak memory: 5.91GB.
PID: 335624; Command: fastq_pair; Return code: 0; Memory used: 5.254GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_trimmed.fastq` (335998)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 335998; Command: mv; Return code: 0; Memory used: 0.001GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed_dups.fastq` (336000)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 336000; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/dups_repaired.flag` (336001)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 336001; Command: touch; Return code: 0; Memory used: 0.0GB
### Prealignments (06-15 07:50:26) elapsed: 348.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-15 07:50:27) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/human_rDNA_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/human_rDNA_bt2` (336003)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 336003; 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_90/prealignments/H9_PRO-seq_90_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_90/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_R2.fq` (336004)
> `(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_90 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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'
25297086 reads; of these:
25297086 (100.00%) were unpaired; of these:
22674298 (89.63%) aligned 0 times
2622788 (10.37%) aligned exactly 1 time
0 (0.00%) aligned >1 times
10.37% overall alignment rate
> `Aligned_reads_human_rDNA` 5245576.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 10.29 PEPPRO _RES_
### Map to human_rDNA (06-15 07:54:33) elapsed: 246.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/human_rDNA_dups_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/human_rDNA_dups_bt2` (336273)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 336273; Command: mkfifo; Return code: 0; Memory used: 0.0GB
File not added to cleanup: prealignments/human_rDNA_dups_bt2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_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_90/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_dups_R2.fq` (336274)
> `(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_90 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/fastq/H9_PRO-seq_90_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)`
not gzipping output
2622788 reads skipped
0 reads lost
File not added to cleanup: prealignments/human_rDNA_dups_bt2
### Map to genome (06-15 07:58:04) elapsed: 211.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_fail_qc_dups.bam
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort.bam`
> `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_90 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_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_90/aligned_hg38/tmp6n7q80nc -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_temp.bam` (336675,336676,336677)
2051450 reads skipped
0 reads lost
22674298 reads; of these:
22674298 (100.00%) were paired; of these:
9399583 (41.45%) aligned concordantly 0 times
10886810 (48.01%) aligned concordantly exactly 1 time
2387905 (10.53%) aligned concordantly >1 times
----
9399583 pairs aligned concordantly 0 times; of these:
2091316 (22.25%) aligned discordantly 1 time
----
7308267 pairs aligned 0 times concordantly or discordantly; of these:
14616534 mates make up the pairs; of these:
5998097 (41.04%) aligned 0 times
3149397 (21.55%) aligned exactly 1 time
5469040 (37.42%) aligned >1 times
86.77% overall alignment rate
[bam_sort_core] merging from 12 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:46:22. Running peak memory: 5.91GB.
PID: 336676; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 336675; Command: bowtie2; Return code: 0; Memory used: 3.788GB
PID: 336677; Command: samtools; Return code: 0; Memory used: 0.913GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort.bam` (341319)
Command completed. Elapsed time: 0:01:23. Running peak memory: 5.91GB.
PID: 341319; 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_90/aligned_hg38/H9_PRO-seq_90_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 39350499 PEPPRO _RES_
> `QC_filtered_reads` 23000545 PEPPRO _RES_
> `Aligned_reads` 16349954.5 PEPPRO _RES_
> `Alignment_rate` 32.06 PEPPRO _RES_
> `Total_efficiency` 15.7 PEPPRO _RES_
> `Read_depth` 2.95 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort_dups.bam`
> `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_90 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_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_90/aligned_hg38/tmp6n7q80nc -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_temp_dups.bam` (342692,342697,342698)
20878303 reads; of these:
20878303 (100.00%) were paired; of these:
8468903 (40.56%) aligned concordantly 0 times
10204244 (48.87%) aligned concordantly exactly 1 time
2205156 (10.56%) aligned concordantly >1 times
----
8468903 pairs aligned concordantly 0 times; of these:
1966476 (23.22%) aligned discordantly 1 time
----
6502427 pairs aligned 0 times concordantly or discordantly; of these:
13004854 mates make up the pairs; of these:
5435246 (41.79%) aligned 0 times
2954556 (22.72%) aligned exactly 1 time
4615052 (35.49%) aligned >1 times
86.98% overall alignment rate
[bam_sort_core] merging from 11 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:38:37. Running peak memory: 5.91GB.
PID: 342692; Command: bowtie2; Return code: 0; Memory used: 3.762GB
PID: 342697; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 342698; Command: samtools; Return code: 0; Memory used: 0.977GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort_dups.bam` (346945)
Command completed. Elapsed time: 0:01:19. Running peak memory: 5.91GB.
PID: 346945; Command: samtools; Return code: 0; Memory used: 0.018GB
### Compress all unmapped read files (06-15 09:38:22) elapsed: 6018.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_R2.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_R2.fq` (347073)
Command completed. Elapsed time: 0:00:19. Running peak memory: 5.91GB.
PID: 347073; Command: pigz; Return code: 0; Memory used: 0.013GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_R1.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/prealignments/H9_PRO-seq_90_human_rDNA_unmap_R1.fq` (347114)
Command completed. Elapsed time: 0:00:21. Running peak memory: 5.91GB.
PID: 347114; Command: pigz; Return code: 0; Memory used: 0.013GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_temp.bam` (347156)
Command completed. Elapsed time: 0:00:35. Running peak memory: 5.91GB.
PID: 347156; Command: samtools; Return code: 0; Memory used: 0.01GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 756629 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort.bam` (347236)
Command completed. Elapsed time: 0:00:23. Running peak memory: 5.91GB.
PID: 347236; Command: samtools; Return code: 0; Memory used: 0.014GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_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_90/aligned_hg38/chr_sizes.bed` (347282,347283,347284,347285)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 347283; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 347285; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 347282; Command: samtools; Return code: 0; Memory used: 0.011GB
PID: 347284; Command: awk; Return code: 0; Memory used: 0.0GB
> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_noMT.bam` (347287)
Command completed. Elapsed time: 0:00:32. Running peak memory: 5.91GB.
PID: 347287; Command: samtools; Return code: 0; Memory used: 0.019GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort.bam` (347574)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 347574; Command: mv; Return code: 0; Memory used: 0.001GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort.bam` (347575)
Command completed. Elapsed time: 0:00:24. Running peak memory: 5.91GB.
PID: 347575; Command: samtools; Return code: 0; Memory used: 0.013GB
### Split BAM file (06-15 09:40:56) elapsed: 154.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam` (347602,347603)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:17. Running peak memory: 5.91GB.
PID: 347603; Command: samtools; Return code: 0; Memory used: 4.627GB
PID: 347602; Command: samtools; Return code: 0; Memory used: 0.004GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE2.bam` (347924,347925)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:52. Running peak memory: 5.91GB.
PID: 347924; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 347925; Command: samtools; Return code: 0; Memory used: 3.745GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_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_90/aligned_hg38/H9_PRO-seq_90_temp_dups.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_temp_dups.bam` (348964)
Command completed. Elapsed time: 0:00:31. Running peak memory: 5.91GB.
PID: 348964; Command: samtools; Return code: 0; Memory used: 0.012GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_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_90/aligned_hg38/H9_PRO-seq_90_sort_dups.bam`
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort_dups.bam.bai
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_dups_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_dups_PE1.bam` (348998,348999)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:02:09. Running peak memory: 5.91GB.
PID: 348998; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 348999; Command: samtools; Return code: 0; Memory used: 4.465GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_dups_PE2.bam` (349202,349203)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:52. Running peak memory: 5.91GB.
PID: 349202; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 349203; Command: samtools; Return code: 0; Memory used: 3.58GB
### Calculate library complexity (06-15 09:50:27) elapsed: 571.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_preseq_out.txt`
> `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_dups_PE1.bam` (349728)
BAM_INPUT
TOTAL READS = 16739307
COUNTS_SUM = 16739307
DISTINCT READS = 1.35944e+07
DISTINCT COUNTS = 302
MAX COUNT = 25272
COUNTS OF 1 = 1.21094e+07
OBSERVED COUNTS (25273)
1 12109447
2 1009536
3 235059
4 92617
5 47577
6 27424
7 17453
8 11457
9 8401
10 6126
11 4555
12 3543
13 2867
14 2217
15 1761
16 1480
17 1206
18 1066
19 933
20 821
21 720
22 595
23 543
24 462
25 433
26 358
27 352
28 312
29 298
30 244
31 251
32 210
33 209
34 181
35 151
36 142
37 135
38 121
39 138
40 124
41 119
42 133
43 91
44 103
45 87
46 88
47 88
48 81
49 63
50 65
51 75
52 68
53 69
54 59
55 60
56 52
57 50
58 46
59 36
60 28
61 48
62 39
63 46
64 46
65 21
66 31
67 35
68 26
69 29
70 28
71 30
72 19
73 28
74 30
75 25
76 18
77 27
78 21
79 21
80 17
81 22
82 13
83 16
84 24
85 20
86 12
87 20
88 9
89 15
90 22
91 15
92 18
93 12
94 8
95 4
96 11
97 13
98 14
99 12
100 13
101 7
102 10
103 11
104 7
105 6
106 9
107 9
108 9
109 7
110 5
111 7
112 11
113 10
114 9
115 4
116 6
117 7
118 5
119 6
121 10
122 9
123 5
124 5
125 10
126 3
127 5
128 3
129 8
130 2
131 8
132 6
133 6
134 4
135 2
136 3
137 2
138 2
139 4
140 6
141 5
142 6
143 4
144 6
145 5
146 7
147 1
148 3
149 2
150 4
151 1
152 4
153 3
154 4
156 5
157 2
158 4
159 3
161 1
162 3
163 2
164 3
165 5
166 1
167 1
168 1
170 1
171 2
172 1
173 2
174 3
176 3
178 5
179 4
180 1
181 3
182 4
183 2
184 2
185 3
186 3
187 1
188 2
190 3
192 2
193 2
194 4
195 2
196 2
198 3
199 1
200 1
201 4
202 1
204 1
205 1
206 2
207 2
208 3
209 2
210 3
212 1
213 3
214 1
215 1
216 1
219 1
223 2
226 2
231 1
234 2
236 4
237 1
238 1
241 1
242 1
243 2
244 1
245 1
247 2
248 2
250 1
251 1
254 2
262 1
267 1
271 1
272 1
274 1
276 1
280 1
281 1
282 1
283 1
285 1
286 2
288 1
289 2
291 1
292 1
294 2
295 2
296 1
300 1
302 1
310 1
311 2
317 1
325 1
326 1
332 1
333 1
334 1
341 1
344 1
348 1
355 1
357 2
362 1
367 1
389 1
392 1
398 1
402 1
411 1
445 1
448 1
453 1
459 1
461 2
466 1
490 1
493 1
495 1
529 1
623 1
637 1
643 1
646 2
648 1
649 1
772 1
800 1
828 1
878 1
910 1
1059 1
1140 1
1197 1
1468 1
1699 1
1712 1
1716 1
2073 1
2212 1
2338 1
3114 1
4028 1
8278 1
9628 1
12271 1
21870 1
25272 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
Command completed. Elapsed time: 0:01:30. Running peak memory: 5.91GB.
PID: 349728; 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_90/QC_hg38/H9_PRO-seq_90_preseq_yield.txt`
> `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_dups_PE1.bam` (350400)
BAM_INPUT
TOTAL READS = 16739307
DISTINCT READS = 1.35944e+07
DISTINCT COUNTS = 302
MAX COUNT = 25272
COUNTS OF 1 = 1.21094e+07
MAX TERMS = 100
OBSERVED COUNTS (25273)
1 12109447
2 1009536
3 235059
4 92617
5 47577
6 27424
7 17453
8 11457
9 8401
10 6126
11 4555
12 3543
13 2867
14 2217
15 1761
16 1480
17 1206
18 1066
19 933
20 821
21 720
22 595
23 543
24 462
25 433
26 358
27 352
28 312
29 298
30 244
31 251
32 210
33 209
34 181
35 151
36 142
37 135
38 121
39 138
40 124
41 119
42 133
43 91
44 103
45 87
46 88
47 88
48 81
49 63
50 65
51 75
52 68
53 69
54 59
55 60
56 52
57 50
58 46
59 36
60 28
61 48
62 39
63 46
64 46
65 21
66 31
67 35
68 26
69 29
70 28
71 30
72 19
73 28
74 30
75 25
76 18
77 27
78 21
79 21
80 17
81 22
82 13
83 16
84 24
85 20
86 12
87 20
88 9
89 15
90 22
91 15
92 18
93 12
94 8
95 4
96 11
97 13
98 14
99 12
100 13
101 7
102 10
103 11
104 7
105 6
106 9
107 9
108 9
109 7
110 5
111 7
112 11
113 10
114 9
115 4
116 6
117 7
118 5
119 6
121 10
122 9
123 5
124 5
125 10
126 3
127 5
128 3
129 8
130 2
131 8
132 6
133 6
134 4
135 2
136 3
137 2
138 2
139 4
140 6
141 5
142 6
143 4
144 6
145 5
146 7
147 1
148 3
149 2
150 4
151 1
152 4
153 3
154 4
156 5
157 2
158 4
159 3
161 1
162 3
163 2
164 3
165 5
166 1
167 1
168 1
170 1
171 2
172 1
173 2
174 3
176 3
178 5
179 4
180 1
181 3
182 4
183 2
184 2
185 3
186 3
187 1
188 2
190 3
192 2
193 2
194 4
195 2
196 2
198 3
199 1
200 1
201 4
202 1
204 1
205 1
206 2
207 2
208 3
209 2
210 3
212 1
213 3
214 1
215 1
216 1
219 1
223 2
226 2
231 1
234 2
236 4
237 1
238 1
241 1
242 1
243 2
244 1
245 1
247 2
248 2
250 1
251 1
254 2
262 1
267 1
271 1
272 1
274 1
276 1
280 1
281 1
282 1
283 1
285 1
286 2
288 1
289 2
291 1
292 1
294 2
295 2
296 1
300 1
302 1
310 1
311 2
317 1
325 1
326 1
332 1
333 1
334 1
341 1
344 1
348 1
355 1
357 2
362 1
367 1
389 1
392 1
398 1
402 1
411 1
445 1
448 1
453 1
459 1
461 2
466 1
490 1
493 1
495 1
529 1
623 1
637 1
643 1
646 2
648 1
649 1
772 1
800 1
828 1
878 1
910 1
1059 1
1140 1
1197 1
1468 1
1699 1
1712 1
1716 1
2073 1
2212 1
2338 1
3114 1
4028 1
8278 1
9628 1
12271 1
21870 1
25272 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
.....__..__......_.._................._..........__......_...._....._._...___....._..._.._........_................_.....
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]
Command completed. Elapsed time: 0:01:45. Running peak memory: 5.91GB.
PID: 350400; Command: preseq; Return code: 0; Memory used: 0.016GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_preseq_counts.txt`
> `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_preseq_counts.txt` (350557)
Command completed. Elapsed time: 0:00:25. Running peak memory: 5.91GB.
PID: 350557; 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_90/QC_hg38/H9_PRO-seq_90_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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_90/QC_hg38/H9_PRO-seq_90_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_preseq_plot` (350611)
Processing H9_PRO-seq_90
INFO: Found real counts for H9_PRO-seq_90 - Total (M): 17.534903 Unique (M): 16.739307
Library complexity plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.91GB.
PID: 350611; Command: Rscript; Return code: 0; Memory used: 0.32GB
> `Library complexity` QC_hg38/H9_PRO-seq_90_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_90_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_90/QC_hg38/H9_PRO-seq_90_preseq_yield.txt | awk '{print $2}'`
> `Frac_exp_unique_at_10M` 0.8542 PEPPRO _RES_
### Calculate NRF, PBC1, and PBC2 (06-15 09:54:11) elapsed: 224.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam` (350630)
Command completed. Elapsed time: 0:00:14. Running peak memory: 5.91GB.
PID: 350630; Command: samtools; Return code: 0; Memory used: 0.008GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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_90/aligned_hg38/H9_PRO-seq_90_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_bamQC.tsv` (350642)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/tmp_H9_PRO-seq_90_PE1_eyt9l283'
Processing with 12 cores...
Discarding 100 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr14_GL000009v2_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270755v1']
Keeping 95 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270509v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Command completed. Elapsed time: 0:00:14. Running peak memory: 5.91GB.
PID: 350642; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.599GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_bamQC.tsv`
> `NRF` 1.0 PEPPRO _RES_
> `PBC1` 8767451.5 PEPPRO _RES_
> `PBC2` 8767451.5 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_unmap.bam`
> `samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_unmap.bam` (350688)
Command completed. Elapsed time: 0:00:08. Running peak memory: 5.91GB.
PID: 350688; 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_90/aligned_hg38/H9_PRO-seq_90_temp.bam`
> `Unmapped_reads` 5998097 PEPPRO _RES_
### Split BAM by strand (06-15 09:54:53) elapsed: 42.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam` (350731)
Command completed. Elapsed time: 0:01:02. Running peak memory: 5.91GB.
PID: 350731; 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_90/aligned_hg38/H9_PRO-seq_90_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam` (351023)
Command completed. Elapsed time: 0:01:00. Running peak memory: 5.91GB.
PID: 351023; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-15 09:56:54) elapsed: 122.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (351103)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351103; 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_90/QC_hg38/H9_PRO-seq_90_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_90/aligned_hg38/H9_PRO-seq_90_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/H9_PRO-seq_90_plus_TssEnrichment.txt` (351105)
Command completed. Elapsed time: 0:00:06. Running peak memory: 5.91GB.
PID: 351105; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.971GB
> `TSS_coding_score` 33.8 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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_90/aligned_hg38/H9_PRO-seq_90_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/H9_PRO-seq_90_minus_TssEnrichment.txt` (351136)
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.91GB.
PID: 351136; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.949GB
> `TSS_non-coding_score` 12.3 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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_90/QC_hg38/H9_PRO-seq_90_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_minus_TssEnrichment.txt` (351169)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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: 5.91GB.
PID: 351169; Command: Rscript; Return code: 0; Memory used: 0.319GB
> `TSS enrichment` QC_hg38/H9_PRO-seq_90_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_90_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_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_90/QC_hg38/chr_order.txt` (351190,351191,351192,351193)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351190; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 351192; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 351191; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 351193; 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_90/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_keep.txt` (351195)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351195; Command: cut; Return code: 0; Memory used: 0.0GB
### Calculate Pause Index (PI) (06-15 09:57:12) elapsed: 17.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_ensembl_tss.bed` (351197,351198)
Command completed. Elapsed time: 0:00:02. Running peak memory: 5.91GB.
PID: 351197; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 351198; Command: bedtools; Return code: 0; Memory used: 0.095GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_ensembl_gene_body.bed` (351202,351203)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351202; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 351203; Command: bedtools; Return code: 0; Memory used: 0.004GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/H9_PRO-seq_90_TSS_density.bed` (351205,351206,351207,351208)
Command completed. Elapsed time: 0:00:22. Running peak memory: 5.91GB.
PID: 351205; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 351207; Command: sort; Return code: 0; Memory used: 0.012GB
PID: 351206; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 351208; Command: sort; Return code: 0; Memory used: 0.003GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_gene_body_density.bed` (351228,351229,351230)
Command completed. Elapsed time: 0:00:25. Running peak memory: 5.91GB.
PID: 351229; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 351228; Command: bedtools; Return code: 0; Memory used: 0.09GB
PID: 351230; Command: sort; Return code: 0; Memory used: 0.006GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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_90/QC_hg38/H9_PRO-seq_90_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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_90/QC_hg38/tmpf1u59rxb` (351277,351278,351279)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351277; Command: join; Return code: 0; Memory used: 0.001GB
PID: 351279; Command: env; Return code: 0; Memory used: 0.004GB
PID: 351278; 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_90/QC_hg38/tmpf1u59rxb | 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_90/QC_hg38/H9_PRO-seq_90_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.0171122) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/tmpf1u59rxb > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_pause_index.bed` (351285)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351285; 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_90/QC_hg38/H9_PRO-seq_90_pause_index.bed | awk ' { a[i++]=$5; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'`
> `Pause_index` 33.96 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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_90/QC_hg38/H9_PRO-seq_90_pause_index.bed` (351290)
Pause index plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.91GB.
PID: 351290; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `Pause index` QC_hg38/H9_PRO-seq_90_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_90_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_pause_index.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_pause_index.bed` (351311)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351311; Command: pigz; Return code: 0; Memory used: 0.004GB
### Calculate Fraction of Reads in pre-mature mRNA (06-15 09:58:07) elapsed: 55.0 _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_90/aligned_hg38/H9_PRO-seq_90_plus.bam`
16349954.5 6344819
> `Plus_FRiP` 0.39 PEPPRO _RES_
Missing stat 'Minus_FRiP'
> `samtools view -@ 4 -c -L /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam`
16349954.5 5914666
> `Minus_FRiP` 0.36 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_gene_sort.bed` (351355,351356)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 351355; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 351356; Command: bedtools; Return code: 0; Memory used: 0.005GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_gene_coverage.bed` (351359)
Command completed. Elapsed time: 0:00:25. Running peak memory: 5.91GB.
PID: 351359; Command: bedtools; Return code: 0; Memory used: 0.092GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/raw/hg38_annotations.bed.gz` (351380)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351380; 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_90/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/hg38_annotations.bed` (351381)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351381; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 09:59:04) elapsed: 57.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/raw/hg38_annotations.bed` (351390)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 351390; 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_90/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Enhancer_sort.bed` (351392,351393,351394,351395)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 351392; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 351393; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 351395; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 351394; 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_90/QC_hg38/H9_PRO-seq_90_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Enhancer_plus_coverage.bed` (351398)
Command completed. Elapsed time: 0:00:11. Running peak memory: 5.91GB.
PID: 351398; 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_90/QC_hg38/H9_PRO-seq_90_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Enhancer_minus_coverage.bed` (351408)
Command completed. Elapsed time: 0:00:10. Running peak memory: 5.91GB.
PID: 351408; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter_sort.bed` (351418,351419,351420,351421)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351418; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 351419; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 351421; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 351420; 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_90/QC_hg38/H9_PRO-seq_90_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Promoter_plus_coverage.bed` (351424)
Command completed. Elapsed time: 0:00:11. Running peak memory: 5.91GB.
PID: 351424; 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_90/QC_hg38/H9_PRO-seq_90_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Promoter_minus_coverage.bed` (351436)
Command completed. Elapsed time: 0:00:11. Running peak memory: 5.91GB.
PID: 351436; Command: bedtools; Return code: 0; Memory used: 0.018GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter_Flanking_Region"` (351447)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351447; 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_90/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed` (351448,351449,351450,351451)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 351448; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 351450; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 351449; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 351451; 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_90/QC_hg38/H9_PRO-seq_90_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Promoter_Flanking_Region_plus_coverage.bed` (351454)
Command completed. Elapsed time: 0:00:11. Running peak memory: 5.91GB.
PID: 351454; 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_90/QC_hg38/H9_PRO-seq_90_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Promoter_Flanking_Region_minus_coverage.bed` (351472)
Command completed. Elapsed time: 0:00:11. Running peak memory: 5.91GB.
PID: 351472; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/5_UTR"` (351722)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351722; 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_90/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/5_UTR_sort.bed` (351723,351724,351725,351726)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 351723; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 351724; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 351726; Command: bedtools; Return code: 0; Memory used: 0.01GB
PID: 351725; 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_90/QC_hg38/H9_PRO-seq_90_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_5_UTR_plus_coverage.bed` (351728)
Command completed. Elapsed time: 0:00:11. Running peak memory: 5.91GB.
PID: 351728; 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_90/QC_hg38/H9_PRO-seq_90_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_5_UTR_minus_coverage.bed` (351739)
Command completed. Elapsed time: 0:00:10. Running peak memory: 5.91GB.
PID: 351739; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/3_UTR"` (351749)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 351749; 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_90/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/3_UTR_sort.bed` (351750,351751,351752,351753)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 351750; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 351751; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 351753; Command: bedtools; Return code: 0; Memory used: 0.01GB
PID: 351752; 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_90/QC_hg38/H9_PRO-seq_90_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_3_UTR_plus_coverage.bed` (351756)
Command completed. Elapsed time: 0:00:11. Running peak memory: 5.91GB.
PID: 351756; Command: bedtools; Return code: 0; Memory used: 0.011GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_3_UTR_minus_coverage.bed` (351766)
Command completed. Elapsed time: 0:00:10. Running peak memory: 5.91GB.
PID: 351766; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Exon_sort.bed` (351778,351779,351780,351781)
Command completed. Elapsed time: 0:00:03. Running peak memory: 5.91GB.
PID: 351778; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 351779; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 351781; Command: bedtools; Return code: 0; Memory used: 0.172GB
PID: 351780; 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_90/QC_hg38/H9_PRO-seq_90_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Exon_plus_coverage.bed` (351785)
Command completed. Elapsed time: 0:00:12. Running peak memory: 5.91GB.
PID: 351785; Command: bedtools; Return code: 0; Memory used: 0.013GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Exon_minus_coverage.bed` (351808)
Command completed. Elapsed time: 0:00:12. Running peak memory: 5.91GB.
PID: 351808; Command: bedtools; Return code: 0; Memory used: 0.013GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Intron_sort.bed` (351820,351821,351822,351823)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 351820; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 351822; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 351821; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 351823; Command: bedtools; Return code: 0; Memory used: 0.082GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Intron_plus_coverage.bed` (351829)
Command completed. Elapsed time: 0:00:13. Running peak memory: 5.91GB.
PID: 351829; Command: bedtools; Return code: 0; Memory used: 0.019GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Intron_minus_coverage.bed` (351844)
Command completed. Elapsed time: 0:00:12. Running peak memory: 5.91GB.
PID: 351844; Command: bedtools; Return code: 0; Memory used: 0.031GB
### Plot cFRiF/FRiF (06-15 10:01:48) elapsed: 165.0 _TIME_
> `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_90 -z 3099922541 -n 8950537 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Intron_plus_coverage.bed` (351882)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:34. Running peak memory: 5.91GB.
PID: 351882; Command: Rscript; Return code: 0; Memory used: 0.466GB
> `cFRiF` QC_hg38/H9_PRO-seq_90_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_90_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_90 -z 3099922541 -n 8950537 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_Intron_plus_coverage.bed` (351973)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:25. Running peak memory: 5.91GB.
PID: 351973; Command: Rscript; Return code: 0; Memory used: 0.458GB
> `FRiF` QC_hg38/H9_PRO-seq_90_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_90_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-15 10:02:48) elapsed: 60.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_exons_sort.bed` (352021,352022)
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.91GB.
PID: 352022; Command: bedtools; Return code: 0; Memory used: 0.1GB
PID: 352021; Command: grep; Return code: 0; Memory used: 0.004GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/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_90/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_introns_sort.bed` (352028,352029,352030)
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.91GB.
PID: 352028; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 352030; Command: bedtools; Return code: 0; Memory used: 0.004GB
PID: 352029; Command: bedtools; Return code: 0; Memory used: 0.035GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_exons_coverage.bed` (352036)
Command completed. Elapsed time: 0:00:21. Running peak memory: 5.91GB.
PID: 352036; Command: bedtools; Return code: 0; Memory used: 0.015GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_introns_coverage.bed` (352054)
Command completed. Elapsed time: 0:00:23. Running peak memory: 5.91GB.
PID: 352054; Command: bedtools; Return code: 0; Memory used: 0.08GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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]/16.3499545)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_exons_rpkm.bed` (352079,352080,352081)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 352079; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 352081; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 352080; 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_90/QC_hg38/H9_PRO-seq_90_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]/16.3499545)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_introns_rpkm.bed` (352083,352084,352085)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.91GB.
PID: 352083; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 352085; Command: sort; Return code: 0; Memory used: 0.003GB
PID: 352084; 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_90/QC_hg38/H9_PRO-seq_90_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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_90/QC_hg38/H9_PRO-seq_90_exon_intron_ratios.bed` (352088,352089,352090)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 352088; Command: join; Return code: 0; Memory used: 0.001GB
PID: 352090; Command: sort; Return code: 0; Memory used: 0.005GB
PID: 352089; 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_90/QC_hg38/H9_PRO-seq_90_exon_intron_ratios.bed | sort -n | awk ' { a[i++]=$1; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'`
> `mRNA_contamination` 1.29 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_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_90/QC_hg38/H9_PRO-seq_90_exon_intron_ratios.bed --annotate` (352096)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.91GB.
PID: 352096; Command: Rscript; Return code: 0; Memory used: 0.317GB
> `mRNA contamination` QC_hg38/H9_PRO-seq_90_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_90_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_exon_intron_ratios.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/QC_hg38/H9_PRO-seq_90_exon_intron_ratios.bed` (352116)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.91GB.
PID: 352116; Command: pigz; Return code: 0; Memory used: 0.003GB
### Produce bigWig files (06-15 10:03:48) elapsed: 60.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_plus.bam` (352125)
Command completed. Elapsed time: 0:00:06. Running peak memory: 5.91GB.
PID: 352125; Command: samtools; Return code: 0; Memory used: 0.01GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_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_90/signal_hg38/H9_PRO-seq_90_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 16349954.5` (352131)
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_90/aligned_hg38/H9_PRO-seq_90_plus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_90_plus_cuttrace_rfo82le1'
Processing with 4 cores...
stdin is empty of data
Discarding 112 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr14_GL000009v2_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1']
Keeping 83 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 83 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_plus_exact_body_0-mer.bw'
Merging 83 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:07:01. Running peak memory: 5.91GB.
PID: 352131; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.6GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_minus.bam` (353975)
Command completed. Elapsed time: 0:00:06. Running peak memory: 5.91GB.
PID: 353975; Command: samtools; Return code: 0; Memory used: 0.01GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/aligned_hg38/H9_PRO-seq_90_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_90/signal_hg38/H9_PRO-seq_90_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 16349954.5` (353985)
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_90/aligned_hg38/H9_PRO-seq_90_minus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_90_minus_cuttrace_huwmlmjq'
Processing with 4 cores...
stdin is empty of data
Discarding 113 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr14_GL000009v2_random', 'chr14_KI270723v1_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270755v1']
Keeping 82 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270509v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 82 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_minus_exact_body_0-mer.bw'
Merging 82 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_90/signal_hg38/H9_PRO-seq_90_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:07:13. Running peak memory: 5.91GB.
PID: 353985; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.361GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 3:00:51
* Total elapsed time (all runs): 5:15:08
* Peak memory (this run): 5.9105 GB
* Pipeline completed time: 2020-06-15 10:18:16