### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_70 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_70pct_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_70pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba27-33c1
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/
* Pipeline started at: (06-15 07:17:18) elapsed: 1.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `12`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_70pct_PE1.fastq.gz']`
* `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_70pct_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_70`
* `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_70pct_PE1.fastq.gz
Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_70pct_PE2.fastq.gz
> `File_mb` 1677.91 PEPPRO _RES_
> `Read_type` PAIRED PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-15 07:17:20) elapsed: 1.0 _TIME_
Number of input file sets: 2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/H9_PRO-seq_70_R1.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_70pct_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/H9_PRO-seq_70_R1.fastq.gz` (420358)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 420358; 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_70/raw/H9_PRO-seq_70_R1.fastq.gz'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/H9_PRO-seq_70_R2.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_70pct_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/H9_PRO-seq_70_R2.fastq.gz` (420361)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 420361; 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_70/raw/H9_PRO-seq_70_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_70/fastq/H9_PRO-seq_70_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2.fastq`
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/H9_PRO-seq_70_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1.fastq` (420364)
Command completed. Elapsed time: 0:02:04. Running peak memory: 0.002GB.
PID: 420364; 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_70/raw/H9_PRO-seq_70_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2.fastq` (420497)
Command completed. Elapsed time: 0:01:35. Running peak memory: 0.002GB.
PID: 420497; Command: pigz; Return code: 0; Memory used: 0.002GB
> `Raw_reads` 81008246 PEPPRO _RES_
> `Fastq_reads` 81008246 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/H9_PRO-seq_70_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/H9_PRO-seq_70_R2.fastq.gz']
### FASTQ processing: (06-15 07:22:29) elapsed: 310.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_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_70/fastq/H9_PRO-seq_70_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/cutadapt/H9_PRO-seq_70_R1_cutadapt.txt` (421060)
Command completed. Elapsed time: 0:01:26. Running peak memory: 3.108GB.
PID: 421060; Command: cutadapt; Return code: 0; Memory used: 3.108GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq` (421227,421228)
Command completed. Elapsed time: 0:00:24. Running peak memory: 3.108GB.
PID: 421227; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 421228; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 19833681 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_70/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq` (421286)
Started analysis of H9_PRO-seq_70_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_70_R1_processed.fastq
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Approx 25% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 35% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_70_R1_processed.fastq
Analysis complete for H9_PRO-seq_70_R1_processed.fastq
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f91aa8a2bd4, pid=421286, tid=0x00007f91798d3700
#
# 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+0x418bd4] ciEnv::get_field_by_index(ciInstanceKlass*, int)+0x94
#
# Core dump written. Default location: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/core or core.421286
#
# An error report file with more information is saved as:
# /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/hs_err_pid421286.log
[thread 140262776989440 also had an error]
# [ timer expired, abort... ]
Command completed. Elapsed time: 0:02:42. Running peak memory: 3.108GB.
PID: 421286; Command: fastqc; Return code: -6; Memory used: 0.216GB
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_70_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_70/fastq/H9_PRO-seq_70_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_70/fastq/H9_PRO-seq_70_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_noadap.fastq` (421765)
[INFO][0m 1700774 duplicated records removed
Command completed. Elapsed time: 0:00:31. Running peak memory: 3.108GB.
PID: 421765; Command: seqkit; Return code: 0; Memory used: 1.035GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_trimmed.fastq` (421810,421811)
Command completed. Elapsed time: 0:00:22. Running peak memory: 3.108GB.
PID: 421810; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 421811; 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_70/cutadapt/H9_PRO-seq_70_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 32096850.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/cutadapt/H9_PRO-seq_70_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_70/cutadapt/H9_PRO-seq_70_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 20028832.0 PEPPRO _RES_
> `Duplicate_reads` 1700774.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 49.4489 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/processed_R1.flag` (422058)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.108GB.
PID: 422058; Command: touch; Return code: 0; Memory used: 0.002GB
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_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_70/fastq/H9_PRO-seq_70_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/cutadapt/H9_PRO-seq_70_R2_cutadapt.txt` (422060)
Command completed. Elapsed time: 0:01:11. Running peak memory: 3.416GB.
PID: 422060; Command: cutadapt; Return code: 0; Memory used: 3.416GB
> `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed.fastq` (422176,422177)
Command completed. Elapsed time: 0:00:27. Running peak memory: 3.416GB.
PID: 422176; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 422177; Command: seqtk; Return code: 0; Memory used: 0.002GB
Evaluating read trimming
> `Trimmed_reads` 39667362 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_70/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq` (422468)
Started analysis of H9_PRO-seq_70_R1_processed.fastq
Approx 5% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 10% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 15% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 20% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 25% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 30% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 35% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 40% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 45% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 50% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 55% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 60% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 65% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 70% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 75% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 80% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 85% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 90% complete for H9_PRO-seq_70_R1_processed.fastq
Approx 95% complete for H9_PRO-seq_70_R1_processed.fastq
Analysis complete for H9_PRO-seq_70_R1_processed.fastq
Command completed. Elapsed time: 0:00:38. Running peak memory: 3.416GB.
PID: 422468; Command: fastqc; Return code: 0; Memory used: 0.166GB
> `FastQC report r1` fastqc/H9_PRO-seq_70_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_70/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed.fastq` (422521)
Started analysis of H9_PRO-seq_70_R2_trimmed.fastq
Approx 5% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 10% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 15% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 20% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 25% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 30% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 35% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 40% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 45% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 50% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 55% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 60% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 65% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 70% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 75% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 80% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 85% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 90% complete for H9_PRO-seq_70_R2_trimmed.fastq
Approx 95% complete for H9_PRO-seq_70_R2_trimmed.fastq
Analysis complete for H9_PRO-seq_70_R2_trimmed.fastq
Command completed. Elapsed time: 0:00:48. Running peak memory: 3.416GB.
PID: 422521; Command: fastqc; Return code: 0; Memory used: 0.17GB
> `FastQC report r2` fastqc/H9_PRO-seq_70_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_70/cutadapt/H9_PRO-seq_70.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/cutadapt/H9_PRO-seq_70.histogram`
> `fastq_pair -t 72907421 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_noadap.fastq` (422735)
Left paired: 20333657 Right paired: 20333657
Left single: 141634 Right single: 1875182
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_noadap.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_noadap.fastq.single.fq
Command completed. Elapsed time: 0:02:12. Running peak memory: 4.435GB.
PID: 422735; Command: fastq_pair; Return code: 0; Memory used: 4.435GB
> `flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_noadap.fastq.paired.fq -o H9_PRO-seq_70 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/cutadapt` (422905)
Command completed. Elapsed time: 0:00:45. Running peak memory: 4.435GB.
PID: 422905; Command: flash; Return code: 0; Memory used: 0.116GB
### Plot adapter insertion distribution (06-15 07:34:46) elapsed: 737.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/cutadapt/H9_PRO-seq_70_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_70/cutadapt/H9_PRO-seq_70.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/cutadapt -u 8` (423091)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 4.435GB.
PID: 423091; Command: Rscript; Return code: 0; Memory used: 0.204GB
> `Adapter insertion distribution` cutadapt/H9_PRO-seq_70_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_70_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_70/cutadapt/H9_PRO-seq_70.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 07:34:53) elapsed: 7.0 _TIME_
> `awk '{ if (($1-8) == 10) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/cutadapt/H9_PRO-seq_70.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_70/cutadapt/H9_PRO-seq_70.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_70/cutadapt/H9_PRO-seq_70.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_70/cutadapt/H9_PRO-seq_70.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_70/cutadapt/H9_PRO-seq_70.hist`
> `Degradation_ratio` 1.0311 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed_dups.fastq`
> `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed_dups.fastq` (423122)
Command completed. Elapsed time: 0:00:23. Running peak memory: 4.435GB.
PID: 423122; 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_70/fastq/processed_R2.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/processed_R2.flag` (423359)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 423359; 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_70/fastq/repaired.flag`
> `fastq_pair -t 72907421 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed.fastq` (423360)
Left paired: 19677250 Right paired: 19677250
Left single: 156431 Right single: 1925340
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed.fastq.single.fq
Command completed. Elapsed time: 0:01:20. Running peak memory: 4.435GB.
PID: 423360; Command: fastq_pair; Return code: 0; Memory used: 3.441GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq` (423440)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 423440; Command: mv; Return code: 0; Memory used: 0.002GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed.fastq` (423441)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 423441; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/repaired.flag` (423442)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 423442; 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_70/fastq/dups_repaired.flag`
> `fastq_pair -t 72907421 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed_dups.fastq` (423443)
Left paired: 18110619 Right paired: 18110619
Left single: 116445 Right single: 3491971
Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed_dups.fastq.paired.fq.
Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed_dups.fastq.single.fq
Command completed. Elapsed time: 0:01:20. Running peak memory: 4.435GB.
PID: 423443; Command: fastq_pair; Return code: 0; Memory used: 3.305GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_trimmed.fastq` (423547)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 423547; Command: mv; Return code: 0; Memory used: 0.002GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed_dups.fastq` (423549)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 423549; Command: mv; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/dups_repaired.flag` (423550)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 423550; Command: touch; Return code: 0; Memory used: 0.0GB
### Prealignments (06-15 07:37:58) elapsed: 185.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-15 07:37:58) elapsed: 0.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/human_rDNA_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/human_rDNA_bt2` (423551)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 423551; Command: mkfifo; Return code: 0; Memory used: 0.001GB
File not added to cleanup: prealignments/human_rDNA_bt2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_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_70/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_R2.fq` (423552)
> `(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_70 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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'
19677250 reads; of these:
19677250 (100.00%) were unpaired; of these:
17637617 (89.63%) aligned 0 times
2039633 (10.37%) aligned exactly 1 time
0 (0.00%) aligned >1 times
10.37% overall alignment rate
> `Aligned_reads_human_rDNA` 4079266.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 10.28 PEPPRO _RES_
### Map to human_rDNA (06-15 07:39:58) elapsed: 120.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/human_rDNA_dups_bt2`
> `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/human_rDNA_dups_bt2` (423686)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 423686; Command: mkfifo; Return code: 0; Memory used: 0.002GB
File not added to cleanup: prealignments/human_rDNA_dups_bt2
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_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_70/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_dups_R2.fq` (423687)
> `(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_70 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/fastq/H9_PRO-seq_70_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)`
not gzipping output
2039633 reads skipped
0 reads lost
File not added to cleanup: prealignments/human_rDNA_dups_bt2
### Map to genome (06-15 07:41:52) elapsed: 114.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_fail_qc_dups.bam
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort.bam`
> `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_70 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_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_70/aligned_hg38/tmpl0o9htnc -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_temp.bam` (424062,424063,424064)
1636542 reads skipped
0 reads lost
17637617 reads; of these:
17637617 (100.00%) were paired; of these:
7312132 (41.46%) aligned concordantly 0 times
8468481 (48.01%) aligned concordantly exactly 1 time
1857004 (10.53%) aligned concordantly >1 times
----
7312132 pairs aligned concordantly 0 times; of these:
1626933 (22.25%) aligned discordantly 1 time
----
5685199 pairs aligned 0 times concordantly or discordantly; of these:
11370398 mates make up the pairs; of these:
4666787 (41.04%) aligned 0 times
2450638 (21.55%) aligned exactly 1 time
4252973 (37.40%) aligned >1 times
86.77% overall alignment rate
[bam_sort_core] merging from 10 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:30:01. Running peak memory: 4.435GB.
PID: 424062; Command: bowtie2; Return code: 0; Memory used: 3.77GB
PID: 424063; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 424064; Command: samtools; Return code: 0; Memory used: 0.897GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort.bam` (427025)
Command completed. Elapsed time: 0:01:01. Running peak memory: 4.435GB.
PID: 427025; 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_70/aligned_hg38/H9_PRO-seq_70_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 30608447 PEPPRO _RES_
> `QC_filtered_reads` 17889191 PEPPRO _RES_
> `Aligned_reads` 12719256.0 PEPPRO _RES_
> `Alignment_rate` 32.06 PEPPRO _RES_
> `Total_efficiency` 15.7 PEPPRO _RES_
> `Read_depth` 2.64 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort_dups.bam`
> `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_70 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_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_70/aligned_hg38/tmpl0o9htnc -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_temp_dups.bam` (428504,428505,428506)
16474077 reads; of these:
16474077 (100.00%) were paired; of these:
6685077 (40.58%) aligned concordantly 0 times
8047929 (48.85%) aligned concordantly exactly 1 time
1741071 (10.57%) aligned concordantly >1 times
----
6685077 pairs aligned concordantly 0 times; of these:
1550215 (23.19%) aligned discordantly 1 time
----
5134862 pairs aligned 0 times concordantly or discordantly; of these:
10269724 mates make up the pairs; of these:
4278230 (41.66%) aligned 0 times
2328888 (22.68%) aligned exactly 1 time
3662606 (35.66%) aligned >1 times
87.02% overall alignment rate
[bam_sort_core] merging from 9 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:28:37. Running peak memory: 4.435GB.
PID: 428505; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 428504; Command: bowtie2; Return code: 0; Memory used: 3.756GB
PID: 428506; Command: samtools; Return code: 0; Memory used: 0.897GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort_dups.bam` (433052)
Command completed. Elapsed time: 0:00:57. Running peak memory: 4.435GB.
PID: 433052; Command: samtools; Return code: 0; Memory used: 0.018GB
### Compress all unmapped read files (06-15 08:52:27) elapsed: 4234.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_R2.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_R2.fq` (433659)
Command completed. Elapsed time: 0:00:15. Running peak memory: 4.435GB.
PID: 433659; Command: pigz; Return code: 0; Memory used: 0.009GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_R1.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/prealignments/H9_PRO-seq_70_human_rDNA_unmap_R1.fq` (433687)
Command completed. Elapsed time: 0:00:17. Running peak memory: 4.435GB.
PID: 433687; Command: pigz; Return code: 0; Memory used: 0.009GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_temp.bam` (433735)
Command completed. Elapsed time: 0:00:26. Running peak memory: 4.435GB.
PID: 433735; Command: samtools; Return code: 0; Memory used: 0.013GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 589030 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort.bam` (433805)
Command completed. Elapsed time: 0:00:19. Running peak memory: 4.435GB.
PID: 433805; Command: samtools; Return code: 0; Memory used: 0.015GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_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_70/aligned_hg38/chr_sizes.bed` (433821,433822,433823,433824)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 433823; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 433821; Command: samtools; Return code: 0; Memory used: 0.008GB
PID: 433824; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 433822; Command: cut; Return code: 0; Memory used: 0.001GB
> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_noMT.bam` (433826)
Command completed. Elapsed time: 0:00:24. Running peak memory: 4.435GB.
PID: 433826; Command: samtools; Return code: 0; Memory used: 0.019GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort.bam` (433870)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 433870; Command: mv; Return code: 0; Memory used: 0.001GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort.bam` (433872)
Command completed. Elapsed time: 0:00:19. Running peak memory: 4.435GB.
PID: 433872; Command: samtools; Return code: 0; Memory used: 0.015GB
### Split BAM file (06-15 08:54:26) elapsed: 119.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam` (433890,433891)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:44. Running peak memory: 4.435GB.
PID: 433890; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 433891; Command: samtools; Return code: 0; Memory used: 3.638GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE2.bam` (434298,434299)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:30. Running peak memory: 4.435GB.
PID: 434298; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 434299; Command: samtools; Return code: 0; Memory used: 2.919GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_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_70/aligned_hg38/H9_PRO-seq_70_temp_dups.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_temp_dups.bam` (434564)
Command completed. Elapsed time: 0:00:24. Running peak memory: 4.435GB.
PID: 434564; Command: samtools; Return code: 0; Memory used: 0.014GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_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_70/aligned_hg38/H9_PRO-seq_70_sort_dups.bam`
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort_dups.bam.bai
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_dups_PE2.bam`
> `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_dups_PE1.bam` (434635,434636)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:42. Running peak memory: 4.435GB.
PID: 434635; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 434636; Command: samtools; Return code: 0; Memory used: 3.523GB
> `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_dups_PE2.bam` (435108,435110)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...
Command completed. Elapsed time: 0:01:28. Running peak memory: 4.435GB.
PID: 435108; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 435110; Command: samtools; Return code: 0; Memory used: 2.827GB
### Calculate library complexity (06-15 09:01:55) elapsed: 449.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_preseq_out.txt`
> `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_dups_PE1.bam` (435289)
BAM_INPUT
TOTAL READS = 13202733
COUNTS_SUM = 13202733
DISTINCT READS = 1.0987e+07
DISTINCT COUNTS = 260
MAX COUNT = 20256
COUNTS OF 1 = 9.91483e+06
OBSERVED COUNTS (20257)
1 9914831
2 738808
3 167534
4 65093
5 32981
6 18819
7 12049
8 7932
9 5463
10 4029
11 3004
12 2254
13 1773
14 1476
15 1227
16 1023
17 847
18 730
19 606
20 504
21 458
22 442
23 322
24 341
25 283
26 258
27 220
28 230
29 188
30 170
31 142
32 147
33 133
34 131
35 126
36 108
37 109
38 110
39 111
40 96
41 78
42 71
43 65
44 53
45 54
46 75
47 50
48 66
49 56
50 46
51 35
52 39
53 41
54 32
55 30
56 31
57 33
58 36
59 41
60 32
61 38
62 26
63 28
64 22
65 26
66 21
67 15
68 21
69 17
70 19
71 21
72 18
73 17
74 13
75 21
76 11
77 20
78 11
79 11
80 10
81 9
82 13
83 10
84 10
85 10
86 13
87 13
88 9
89 8
90 12
91 10
92 11
93 6
94 3
95 7
96 7
97 8
98 7
99 7
100 10
101 9
102 6
103 6
104 6
105 5
106 3
107 5
108 8
109 5
110 7
111 3
112 7
113 4
114 4
115 2
116 3
117 5
118 6
119 5
120 3
121 5
122 4
123 8
124 1
125 5
126 3
127 2
128 2
129 5
130 2
131 1
132 3
133 2
135 6
136 2
137 1
138 3
139 2
140 1
142 3
143 7
144 2
145 2
146 2
147 3
148 6
149 1
150 6
151 2
153 5
154 2
155 3
156 2
157 6
158 1
160 1
161 3
162 2
163 2
164 2
165 1
166 4
167 1
171 1
172 1
173 1
176 2
178 1
180 1
181 2
182 2
184 1
185 3
188 1
189 2
190 2
192 1
193 1
194 2
196 1
197 1
201 2
202 2
203 1
204 1
210 1
212 2
214 1
215 1
223 1
225 2
226 2
227 1
228 2
231 1
232 2
234 2
236 1
237 1
238 1
241 1
243 1
244 2
245 1
246 1
247 1
254 1
255 1
261 1
262 3
266 1
267 2
271 1
280 1
285 1
295 1
303 1
304 1
312 1
316 1
330 1
335 1
339 1
354 1
360 1
361 1
371 1
374 2
375 1
395 1
400 1
417 1
493 1
498 1
499 1
503 2
505 1
507 1
633 1
641 1
652 1
680 1
730 1
828 1
928 1
944 1
1153 1
1359 1
1363 1
1386 1
1655 1
1734 1
1854 1
2497 1
3223 1
6517 1
7685 1
9775 1
18952 1
20256 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
Command completed. Elapsed time: 0:01:12. Running peak memory: 4.435GB.
PID: 435289; 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_70/QC_hg38/H9_PRO-seq_70_preseq_yield.txt`
> `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_dups_PE1.bam` (435463)
BAM_INPUT
TOTAL READS = 13202733
DISTINCT READS = 1.0987e+07
DISTINCT COUNTS = 260
MAX COUNT = 20256
COUNTS OF 1 = 9.91483e+06
MAX TERMS = 100
OBSERVED COUNTS (20257)
1 9914831
2 738808
3 167534
4 65093
5 32981
6 18819
7 12049
8 7932
9 5463
10 4029
11 3004
12 2254
13 1773
14 1476
15 1227
16 1023
17 847
18 730
19 606
20 504
21 458
22 442
23 322
24 341
25 283
26 258
27 220
28 230
29 188
30 170
31 142
32 147
33 133
34 131
35 126
36 108
37 109
38 110
39 111
40 96
41 78
42 71
43 65
44 53
45 54
46 75
47 50
48 66
49 56
50 46
51 35
52 39
53 41
54 32
55 30
56 31
57 33
58 36
59 41
60 32
61 38
62 26
63 28
64 22
65 26
66 21
67 15
68 21
69 17
70 19
71 21
72 18
73 17
74 13
75 21
76 11
77 20
78 11
79 11
80 10
81 9
82 13
83 10
84 10
85 10
86 13
87 13
88 9
89 8
90 12
91 10
92 11
93 6
94 3
95 7
96 7
97 8
98 7
99 7
100 10
101 9
102 6
103 6
104 6
105 5
106 3
107 5
108 8
109 5
110 7
111 3
112 7
113 4
114 4
115 2
116 3
117 5
118 6
119 5
120 3
121 5
122 4
123 8
124 1
125 5
126 3
127 2
128 2
129 5
130 2
131 1
132 3
133 2
135 6
136 2
137 1
138 3
139 2
140 1
142 3
143 7
144 2
145 2
146 2
147 3
148 6
149 1
150 6
151 2
153 5
154 2
155 3
156 2
157 6
158 1
160 1
161 3
162 2
163 2
164 2
165 1
166 4
167 1
171 1
172 1
173 1
176 2
178 1
180 1
181 2
182 2
184 1
185 3
188 1
189 2
190 2
192 1
193 1
194 2
196 1
197 1
201 2
202 2
203 1
204 1
210 1
212 2
214 1
215 1
223 1
225 2
226 2
227 1
228 2
231 1
232 2
234 2
236 1
237 1
238 1
241 1
243 1
244 2
245 1
246 1
247 1
254 1
255 1
261 1
262 3
266 1
267 2
271 1
280 1
285 1
295 1
303 1
304 1
312 1
316 1
330 1
335 1
339 1
354 1
360 1
361 1
371 1
374 2
375 1
395 1
400 1
417 1
493 1
498 1
499 1
503 2
505 1
507 1
633 1
641 1
652 1
680 1
730 1
828 1
928 1
944 1
1153 1
1359 1
1363 1
1386 1
1655 1
1734 1
1854 1
2497 1
3223 1
6517 1
7685 1
9775 1
18952 1
20256 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
....................................................................................................
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]
Command completed. Elapsed time: 0:01:21. Running peak memory: 4.435GB.
PID: 435463; 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_70/QC_hg38/H9_PRO-seq_70_preseq_counts.txt`
> `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_preseq_counts.txt` (435574)
Command completed. Elapsed time: 0:00:20. Running peak memory: 4.435GB.
PID: 435574; 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_70/QC_hg38/H9_PRO-seq_70_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_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_70/QC_hg38/H9_PRO-seq_70_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_preseq_plot` (435613)
Processing H9_PRO-seq_70
INFO: Found real counts for H9_PRO-seq_70 - Total (M): 13.641283 Unique (M): 13.202733
Library complexity plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.435GB.
PID: 435613; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `Library complexity` QC_hg38/H9_PRO-seq_70_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_70_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_70/QC_hg38/H9_PRO-seq_70_preseq_yield.txt | awk '{print $2}'`
> `Frac_exp_unique_at_10M` 0.8537 PEPPRO _RES_
### Calculate NRF, PBC1, and PBC2 (06-15 09:04:53) elapsed: 178.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam` (435650)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.435GB.
PID: 435650; 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_70/QC_hg38/H9_PRO-seq_70_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_70/aligned_hg38/H9_PRO-seq_70_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_bamQC.tsv` (435859)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/tmp_H9_PRO-seq_70_PE1_th0jhiqu'
Processing with 12 cores...
Discarding 101 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr14_GL000009v2_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_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 94 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_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: 0:00:12. Running peak memory: 4.435GB.
PID: 435859; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.388GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_bamQC.tsv`
> `NRF` 1.0 PEPPRO _RES_
> `PBC1` 6820641.5 PEPPRO _RES_
> `PBC2` 6820641.5 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_unmap.bam`
> `samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_unmap.bam` (435909)
Command completed. Elapsed time: 0:00:06. Running peak memory: 4.435GB.
PID: 435909; 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_70/aligned_hg38/H9_PRO-seq_70_temp.bam`
> `Unmapped_reads` 4666787 PEPPRO _RES_
### Split BAM by strand (06-15 09:05:26) elapsed: 33.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam` (435959)
Command completed. Elapsed time: 0:00:49. Running peak memory: 4.435GB.
PID: 435959; 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_70/aligned_hg38/H9_PRO-seq_70_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam` (436486)
Command completed. Elapsed time: 0:00:47. Running peak memory: 4.435GB.
PID: 436486; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-15 09:07:01) elapsed: 96.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (436570)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436570; 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_70/QC_hg38/H9_PRO-seq_70_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_70/aligned_hg38/H9_PRO-seq_70_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/H9_PRO-seq_70_plus_TssEnrichment.txt` (436583)
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.435GB.
PID: 436583; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.981GB
> `TSS_coding_score` 33.8 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_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_70/aligned_hg38/H9_PRO-seq_70_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/H9_PRO-seq_70_minus_TssEnrichment.txt` (436634)
Command completed. Elapsed time: 0:00:04. Running peak memory: 4.435GB.
PID: 436634; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 1.103GB
> `TSS_non-coding_score` 12.3 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_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_70/QC_hg38/H9_PRO-seq_70_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_minus_TssEnrichment.txt` (436668)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_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: 4.435GB.
PID: 436668; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `TSS enrichment` QC_hg38/H9_PRO-seq_70_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_70_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_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_70/QC_hg38/chr_order.txt` (436690,436691,436692,436693)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436690; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 436692; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 436691; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 436693; 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_70/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_keep.txt` (436695)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436695; Command: cut; Return code: 0; Memory used: 0.0GB
### Calculate Pause Index (PI) (06-15 09:07:17) elapsed: 16.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_ensembl_tss.bed` (436697,436698)
Command completed. Elapsed time: 0:00:02. Running peak memory: 4.435GB.
PID: 436697; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 436698; Command: bedtools; Return code: 0; Memory used: 0.093GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_ensembl_gene_body.bed` (436702,436703)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436702; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 436703; Command: bedtools; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/H9_PRO-seq_70_TSS_density.bed` (436705,436706,436707,436708)
Command completed. Elapsed time: 0:00:19. Running peak memory: 4.435GB.
PID: 436705; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 436707; Command: sort; Return code: 0; Memory used: 0.01GB
PID: 436706; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 436708; 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_70/QC_hg38/H9_PRO-seq_70_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_gene_body_density.bed` (436725,436726,436727)
Command completed. Elapsed time: 0:00:22. Running peak memory: 4.435GB.
PID: 436726; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 436725; Command: bedtools; Return code: 0; Memory used: 0.077GB
PID: 436727; Command: sort; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_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_70/QC_hg38/H9_PRO-seq_70_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_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_70/QC_hg38/tmpc1j1oqlj` (436757,436758,436759)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436757; Command: join; Return code: 0; Memory used: 0.001GB
PID: 436759; Command: env; Return code: 0; Memory used: 0.004GB
PID: 436758; 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_70/QC_hg38/tmpc1j1oqlj | 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_70/QC_hg38/H9_PRO-seq_70_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.0138162) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/tmpc1j1oqlj > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_pause_index.bed` (436765)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436765; 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_70/QC_hg38/H9_PRO-seq_70_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` 33.69 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_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_70/QC_hg38/H9_PRO-seq_70_pause_index.bed` (436770)
Pause index plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.435GB.
PID: 436770; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `Pause index` QC_hg38/H9_PRO-seq_70_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_70_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_pause_index.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_pause_index.bed` (436791)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436791; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-15 09:08:06) elapsed: 49.0 _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_70/aligned_hg38/H9_PRO-seq_70_plus.bam`
12719256.0 4935879
> `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_70/aligned_hg38/H9_PRO-seq_70_minus.bam`
12719256.0 4602962
> `Minus_FRiP` 0.36 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_gene_sort.bed` (436828,436829)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 436828; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 436829; Command: bedtools; Return code: 0; Memory used: 0.006GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_gene_coverage.bed` (436831)
Command completed. Elapsed time: 0:00:21. Running peak memory: 4.435GB.
PID: 436831; Command: bedtools; Return code: 0; Memory used: 0.079GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/raw/hg38_annotations.bed.gz` (436852)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436852; Command: ln; Return code: 0; Memory used: 0.0GB
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/hg38_annotations.bed` (436853)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436853; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 09:08:53) elapsed: 47.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/raw/hg38_annotations.bed` (436862)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 436862; 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_70/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Enhancer_sort.bed` (436864,436865,436866,436867)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 436864; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 436865; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 436867; Command: bedtools; Return code: 0; Memory used: 0.012GB
PID: 436866; 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_70/QC_hg38/H9_PRO-seq_70_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Enhancer_plus_coverage.bed` (436869)
Command completed. Elapsed time: 0:00:09. Running peak memory: 4.435GB.
PID: 436869; 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_70/QC_hg38/H9_PRO-seq_70_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Enhancer_minus_coverage.bed` (436879)
Command completed. Elapsed time: 0:00:09. Running peak memory: 4.435GB.
PID: 436879; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter_sort.bed` (436890,436891,436892,436893)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 436890; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 436891; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 436893; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 436892; 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_70/QC_hg38/H9_PRO-seq_70_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Promoter_plus_coverage.bed` (436896)
Command completed. Elapsed time: 0:00:10. Running peak memory: 4.435GB.
PID: 436896; 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_70/QC_hg38/H9_PRO-seq_70_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Promoter_minus_coverage.bed` (436968)
Command completed. Elapsed time: 0:00:09. Running peak memory: 4.435GB.
PID: 436968; Command: bedtools; Return code: 0; Memory used: 0.015GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter_Flanking_Region"` (436977)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 436977; 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_70/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter_Flanking_Region_sort.bed` (436978,436979,436980,436981)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 436978; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 436980; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 436979; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 436981; 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_70/QC_hg38/H9_PRO-seq_70_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Promoter_Flanking_Region_plus_coverage.bed` (436984)
Command completed. Elapsed time: 0:00:09. Running peak memory: 4.435GB.
PID: 436984; 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_70/QC_hg38/H9_PRO-seq_70_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Promoter_Flanking_Region_minus_coverage.bed` (436993)
Command completed. Elapsed time: 0:00:09. Running peak memory: 4.435GB.
PID: 436993; Command: bedtools; Return code: 0; Memory used: 0.016GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/5_UTR"` (437013)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 437013; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/5_UTR_sort.bed` (437014,437015,437016,437017)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 437014; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 437015; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 437017; Command: bedtools; Return code: 0; Memory used: 0.03GB
PID: 437016; 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_70/QC_hg38/H9_PRO-seq_70_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_5_UTR_plus_coverage.bed` (437019)
Command completed. Elapsed time: 0:00:09. Running peak memory: 4.435GB.
PID: 437019; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_5_UTR_minus_coverage.bed` (437290)
Command completed. Elapsed time: 0:00:09. Running peak memory: 4.435GB.
PID: 437290; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/3_UTR"` (437313)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 437313; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/3_UTR_sort.bed` (437314,437315,437316,437317)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 437314; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 437315; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 437317; Command: bedtools; Return code: 0; Memory used: 0.034GB
PID: 437316; 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_70/QC_hg38/H9_PRO-seq_70_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_3_UTR_plus_coverage.bed` (437319)
Command completed. Elapsed time: 0:00:09. Running peak memory: 4.435GB.
PID: 437319; 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_70/QC_hg38/H9_PRO-seq_70_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_3_UTR_minus_coverage.bed` (437346)
Command completed. Elapsed time: 0:00:09. Running peak memory: 4.435GB.
PID: 437346; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Exon_sort.bed` (437356,437357,437358,437359)
Command completed. Elapsed time: 0:00:03. Running peak memory: 4.435GB.
PID: 437356; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 437357; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 437359; Command: bedtools; Return code: 0; Memory used: 0.158GB
PID: 437358; 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_70/QC_hg38/H9_PRO-seq_70_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Exon_plus_coverage.bed` (437364)
Command completed. Elapsed time: 0:00:10. Running peak memory: 4.435GB.
PID: 437364; 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_70/QC_hg38/H9_PRO-seq_70_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Exon_minus_coverage.bed` (437383)
Command completed. Elapsed time: 0:00:10. Running peak memory: 4.435GB.
PID: 437383; Command: bedtools; Return code: 0; Memory used: 0.012GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Intron_sort.bed` (437411,437412,437413,437414)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 437411; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 437413; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 437412; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 437414; Command: bedtools; Return code: 0; Memory used: 0.077GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Intron_plus_coverage.bed` (437417)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.435GB.
PID: 437417; Command: bedtools; Return code: 0; Memory used: 0.023GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Intron_minus_coverage.bed` (437437)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.435GB.
PID: 437437; Command: bedtools; Return code: 0; Memory used: 0.028GB
### Plot cFRiF/FRiF (06-15 09:11:17) elapsed: 144.0 _TIME_
> `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_70 -z 3099922541 -n 6962098 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Intron_plus_coverage.bed` (437472)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:35. Running peak memory: 4.435GB.
PID: 437472; Command: Rscript; Return code: 0; Memory used: 0.466GB
> `cFRiF` QC_hg38/H9_PRO-seq_70_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_70_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_70 -z 3099922541 -n 6962098 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_Intron_plus_coverage.bed` (437550)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:26. Running peak memory: 4.435GB.
PID: 437550; Command: Rscript; Return code: 0; Memory used: 0.466GB
> `FRiF` QC_hg38/H9_PRO-seq_70_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_70_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-15 09:12:19) elapsed: 62.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_exons_sort.bed` (438097,438098)
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.435GB.
PID: 438098; Command: bedtools; Return code: 0; Memory used: 0.086GB
PID: 438097; Command: grep; Return code: 0; Memory used: 0.004GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/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_70/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_introns_sort.bed` (438104,438105,438106)
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.435GB.
PID: 438104; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 438106; Command: bedtools; Return code: 0; Memory used: 0.006GB
PID: 438105; Command: bedtools; Return code: 0; Memory used: 0.033GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_exons_coverage.bed` (438113)
Command completed. Elapsed time: 0:00:18. Running peak memory: 4.435GB.
PID: 438113; Command: bedtools; Return code: 0; Memory used: 0.014GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_introns_coverage.bed` (438147)
Command completed. Elapsed time: 0:00:20. Running peak memory: 4.435GB.
PID: 438147; Command: bedtools; Return code: 0; Memory used: 0.066GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_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]/12.719256)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_exons_rpkm.bed` (438184,438185,438186)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 438184; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 438186; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 438185; 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_70/QC_hg38/H9_PRO-seq_70_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]/12.719256)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_introns_rpkm.bed` (438189,438190,438191)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.435GB.
PID: 438189; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 438191; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 438190; 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_70/QC_hg38/H9_PRO-seq_70_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_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_70/QC_hg38/H9_PRO-seq_70_exon_intron_ratios.bed` (438193,438194,438195)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 438193; Command: join; Return code: 0; Memory used: 0.001GB
PID: 438195; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 438194; 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_70/QC_hg38/H9_PRO-seq_70_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_70/QC_hg38/H9_PRO-seq_70_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_70/QC_hg38/H9_PRO-seq_70_exon_intron_ratios.bed --annotate` (438201)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.435GB.
PID: 438201; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `mRNA contamination` QC_hg38/H9_PRO-seq_70_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_70_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_exon_intron_ratios.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/QC_hg38/H9_PRO-seq_70_exon_intron_ratios.bed` (438222)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.435GB.
PID: 438222; Command: pigz; Return code: 0; Memory used: 0.003GB
### Produce bigWig files (06-15 09:13:14) elapsed: 55.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_plus.bam` (438230)
Command completed. Elapsed time: 0:00:06. Running peak memory: 4.435GB.
PID: 438230; Command: samtools; Return code: 0; Memory used: 0.011GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_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_70/signal_hg38/H9_PRO-seq_70_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 12719256.0` (438236)
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_70/aligned_hg38/H9_PRO-seq_70_plus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_70_plus_cuttrace_lwzndau9'
Processing with 4 cores...
stdin is empty of data
Discarding 115 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr5_GL000208v1_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_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1']
Keeping 80 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_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', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_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 80 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_plus_exact_body_0-mer.bw'
Merging 80 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:06:18. Running peak memory: 4.435GB.
PID: 438236; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.382GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_minus.bam` (439527)
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.435GB.
PID: 439527; Command: samtools; Return code: 0; Memory used: 0.011GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/aligned_hg38/H9_PRO-seq_70_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_70/signal_hg38/H9_PRO-seq_70_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 12719256.0` (439532)
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_70/aligned_hg38/H9_PRO-seq_70_minus.bam'
Temporary files will be stored in: 'tmp_H9_PRO-seq_70_minus_cuttrace_uvl4y49i'
Processing with 4 cores...
stdin is empty of data
Discarding 115 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr14_KI270723v1_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1']
Keeping 80 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_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_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 80 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_minus_exact_body_0-mer.bw'
Merging 80 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_70/signal_hg38/H9_PRO-seq_70_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:06:27. Running peak memory: 4.435GB.
PID: 439532; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.424GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 2:08:52
* Total elapsed time (all runs): 3:43:48
* Peak memory (this run): 4.4352 GB
* Pipeline completed time: 2020-06-15 09:26:10