### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name HelaS3_GRO-seq --genome hg38 --input /project/shefflab/data//sra_fastq/SRR1693611.fastq.gz /project/shefflab/data//sra_fastq/SRR1693612.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol GRO --umi-len 0 --scale --prealignments human_rDNA --dirty`
* Compute host: udc-aj37-18c1
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/
* Pipeline started at: (06-11 17:32:09) elapsed: 11.0 _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, 16373 insertions(+), 3522 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//sra_fastq/SRR1693611.fastq.gz', '/project/shefflab/data//sra_fastq/SRR1693612.fastq.gz']`
* `input2`: `None`
* `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`: `False`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `GRO`
* `recover`: `False`
* `sample_name`: `HelaS3_GRO-seq`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `SINGLE`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `0`
* `verbosity`: `None`
----------------------------------------
Local input file: /project/shefflab/data//sra_fastq/SRR1693611.fastq.gz
> `File_mb` 3550.33 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected GRO input
### Merge/link and fastq conversion: (06-11 17:32:11) elapsed: 2.0 _TIME_
Number of input file sets: 1
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz`
> `cat /project/shefflab/data//sra_fastq/SRR1693611.fastq.gz /project/shefflab/data//sra_fastq/SRR1693612.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz` (51527)
Command completed. Elapsed time: 0:00:42. Running peak memory: 0.003GB.
PID: 51527; Command: cat; Return code: 0; Memory used: 0.003GB
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz'
Found .fastq.gz file
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1.fastq`
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1.fastq` (51577)
Command completed. Elapsed time: 0:02:15. Running peak memory: 0.003GB.
PID: 51577; Command: pigz; Return code: 0; Memory used: 0.002GB
> `Raw_reads` 72718941 PEPPRO _RES_
> `Fastq_reads` 72718941 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz']
### FASTQ processing: (06-11 17:38:35) elapsed: 384.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1_processed.fastq`
> `(cutadapt -j 12 -m 2 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt` (52260)
Command completed. Elapsed time: 0:03:25. Running peak memory: 4.586GB.
PID: 52260; Command: cutadapt; Return code: 0; Memory used: 4.586GB
> `seqtk trimfq -b 0 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1_noadap.fastq | seqtk seq -L 2 - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1_processed.fastq` (52745,52746)
Command completed. Elapsed time: 0:02:38. Running peak memory: 4.586GB.
PID: 52745; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 52746; Command: seqtk; Return code: 0; Memory used: 0.002GB
> `grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 22179715.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_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/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 0.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 0.0 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastqc/HelaS3_GRO-seq_R1_processed_fastqc.html`
> `echo '### Calculate the number of trimmed reads'` (54520)
### Calculate the number of trimmed reads
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.586GB.
PID: 54520; Command: echo; Return code: 0; Memory used: 0.0GB
Evaluating read trimming
> `Trimmed_reads` 72718941 PEPPRO _RES_
> `Trim_loss_rate` 0.0 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1_processed.fastq` (55987)
Started analysis of HelaS3_GRO-seq_R1_processed.fastq
Approx 5% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 10% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 15% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 20% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 25% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 30% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 35% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 40% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 45% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 50% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 55% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 60% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 65% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 70% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 75% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 80% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 85% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 90% complete for HelaS3_GRO-seq_R1_processed.fastq
Approx 95% complete for HelaS3_GRO-seq_R1_processed.fastq
Analysis complete for HelaS3_GRO-seq_R1_processed.fastq
Command completed. Elapsed time: 0:03:57. Running peak memory: 4.586GB.
PID: 55987; Command: fastqc; Return code: 0; Memory used: 0.192GB
> `FastQC report r1` fastqc/HelaS3_GRO-seq_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/processed_R1.flag` (57324)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.586GB.
PID: 57324; Command: touch; Return code: 0; Memory used: 0.0GB
### Plot adapter insertion distribution (06-11 17:54:51) elapsed: 976.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_adapter_insertion_distribution.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R cutadapt -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt` (57326)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 4.586GB.
PID: 57326; Command: Rscript; Return code: 0; Memory used: 0.204GB
> `Adapter insertion distribution` cutadapt/HelaS3_GRO-seq_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/HelaS3_GRO-seq_R1_adapter_insertion_distribution.png PEPPRO _OBJ_
Missing stat 'Peak_adapter_insertion_size'
> `awk '/count/,0' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt | awk 'NR>2 {print prev} {prev=$0}' | awk '{if ($3/$2 < 0.01) print $1, $2}' | awk 'BEGIN{max= 0; max_len=0; len=0}{if ($2>0+max) {max=$2; len=$1}; max_len=$1} END{print max_len-len}'`
> `Peak_adapter_insertion_size` 0 PEPPRO _RES_
Missing stat 'Degradation_ratio'
### Calculating degradation ratio (06-11 17:54:58) elapsed: 7.0 _TIME_
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt | awk '{ if ($1 == 10) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt | awk '{ if ($1 == 20) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt | awk '{ if ($1 == 30) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt | awk '{ if ($1 == 40) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt | awk 'END {print $1}'`
> `awk '/count/,0' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_cutadapt.txt | awk 'NR>2 {print prev} {prev=$0}' | awk '{if ($3/$2 < 0.01) print $1, $2}' | awk '{a[NR]=$1; b[NR]=$2; max_len=$1}{if ($1 > max_len) {max_len=$1}} END{ for (i in a) print 1+max_len-a[i], b[i]}' | sort -nk1 | awk '($1 <= 10 && $1 >= 14){degradedSum += $2}; ($1 >= 4 && $1 <= 0){intactSum += $2} END {if (intactSum < 1) {intactSum = 1} print degradedSum/intactSum}'`
> `Degradation_ratio` 0.0 PEPPRO _RES_
### Prealignments (06-11 17:54:58) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-11 17:54:58) elapsed: 0.0 _TIME_
> `(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 HelaS3_GRO-seq -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/prealignments/HelaS3_GRO-seq_human_rDNA_unmap.fq 2>&1 > /dev/null)`
Missing stat 'Aligned_reads_human_rDNA'
72718941 reads; of these:
72718941 (100.00%) were unpaired; of these:
31839185 (43.78%) aligned 0 times
40879756 (56.22%) aligned exactly 1 time
0 (0.00%) aligned >1 times
56.22% overall alignment rate
> `Aligned_reads_human_rDNA` 40879756.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 56.22 PEPPRO _RES_
### Map to genome (06-11 18:03:13) elapsed: 495.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam`
> `bowtie2 -p 12 --very-sensitive --rg-id HelaS3_GRO-seq -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/prealignments/HelaS3_GRO-seq_human_rDNA_unmap.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/tmplwu3sau6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_temp.bam` (59918,59923,59924)
31839185 reads; of these:
31839185 (100.00%) were unpaired; of these:
10809494 (33.95%) aligned 0 times
13023651 (40.90%) aligned exactly 1 time
8006040 (25.15%) aligned >1 times
66.05% overall alignment rate
[bam_sort_core] merging from 8 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:12:23. Running peak memory: 4.586GB.
PID: 59918; Command: bowtie2; Return code: 0; Memory used: 3.666GB
PID: 59923; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 59924; Command: samtools; Return code: 0; Memory used: 0.899GB
> `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam` (63877)
Command completed. Elapsed time: 0:01:41. Running peak memory: 4.586GB.
PID: 63877; 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/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 21029691 PEPPRO _RES_
> `QC_filtered_reads` 6163527 PEPPRO _RES_
> `Aligned_reads` 14866164 PEPPRO _RES_
> `Alignment_rate` 20.44 PEPPRO _RES_
> `Total_efficiency` 20.44 PEPPRO _RES_
> `Read_depth` 2.34 PEPPRO _RES_
### Compress all unmapped read files (06-11 18:26:53) elapsed: 1420.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/prealignments/HelaS3_GRO-seq_human_rDNA_unmap.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/prealignments/HelaS3_GRO-seq_human_rDNA_unmap.fq` (67152)
Command completed. Elapsed time: 0:01:03. Running peak memory: 4.586GB.
PID: 67152; 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/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_temp.bam` (67418)
Command completed. Elapsed time: 0:00:24. Running peak memory: 4.586GB.
PID: 67418; Command: samtools; Return code: 0; Memory used: 0.016GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 1906316 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam` (67506)
Command completed. Elapsed time: 0:00:12. Running peak memory: 4.586GB.
PID: 67506; Command: samtools; Return code: 0; Memory used: 0.007GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_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/HelaS3_GRO-seq/aligned_hg38/chr_sizes.bed` (67553,67554,67555,67556)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.586GB.
PID: 67553; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 67555; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 67554; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 67556; Command: grep; Return code: 0; Memory used: 0.0GB
> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_noMT.bam` (67558)
Command completed. Elapsed time: 0:00:15. Running peak memory: 4.586GB.
PID: 67558; Command: samtools; Return code: 0; Memory used: 0.019GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam` (67633)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.586GB.
PID: 67633; Command: mv; Return code: 0; Memory used: 0.001GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam` (67637)
Command completed. Elapsed time: 0:00:12. Running peak memory: 4.586GB.
PID: 67637; Command: samtools; Return code: 0; Memory used: 0.007GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-`
> `Maximum_read_length` 51 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_
### Calculate NRF, PBC1, and PBC2 (06-11 18:29:41) elapsed: 168.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam.bai`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_bamQC.tsv`
> `/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_bamQC.tsv` (67810)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/tmp_HelaS3_GRO-seq_sort_whhdf766'
Processing with 12 cores...
Discarding 117 chunk(s) of reads: ['chrM', 'chr1_KI270708v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr9_KI270717v1_random', 'chr9_KI270720v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270726v1_random', 'chr22_KI270735v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', '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_GL000220v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrEBV']
Keeping 78 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270725v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270438v1', 'chrUn_KI270538v1', 'chrUn_KI270582v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000224v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270755v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1']
Command completed. Elapsed time: 0:00:21. Running peak memory: 4.586GB.
PID: 67810; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.267GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_bamQC.tsv`
> `NRF` 0.72 PEPPRO _RES_
> `PBC1` 0.91 PEPPRO _RES_
> `PBC2` 13.55 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_unmap.bam`
> `samtools view -b -@ 12 -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_unmap.bam` (68140)
Command completed. Elapsed time: 0:00:12. Running peak memory: 4.586GB.
PID: 68140; Command: samtools; Return code: 0; Memory used: 0.017GB
> `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_temp.bam`
> `Unmapped_reads` 10809494 PEPPRO _RES_
### Split BAM by strand (06-11 18:30:19) elapsed: 38.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam` (68322)
Command completed. Elapsed time: 0:00:57. Running peak memory: 4.586GB.
PID: 68322; Command: samtools; Return code: 0; Memory used: 0.006GB
> `samtools view -bh -f 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam` (68549)
Command completed. Elapsed time: 0:00:54. Running peak memory: 4.586GB.
PID: 68549; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-11 18:32:10) elapsed: 111.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (68757)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.586GB.
PID: 68757; Command: sed; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_plus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_plus_TssEnrichment.txt` (68761)
Command completed. Elapsed time: 0:00:08. Running peak memory: 4.586GB.
PID: 68761; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.509GB
> `TSS_coding_score` 7.3 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_minus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_minus_TssEnrichment.txt` (68819)
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.586GB.
PID: 68819; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.863GB
> `TSS_non-coding_score` 4.1 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSSenrichment.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_minus_TssEnrichment.txt` (68863)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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: 0:00:13. Running peak memory: 4.586GB.
PID: 68863; Command: Rscript; Return code: 0; Memory used: 0.084GB
> `TSS enrichment` QC_hg38/HelaS3_GRO-seq_TSSenrichment.pdf TSS enrichment QC_hg38/HelaS3_GRO-seq_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.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/HelaS3_GRO-seq/QC_hg38/chr_order.txt` (68914,68915,68916,68917)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.586GB.
PID: 68914; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 68916; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 68915; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 68917; Command: awk; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_keep.txt` (68922)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.586GB.
PID: 68922; Command: cut; Return code: 0; Memory used: 0.002GB
### Calculate Pause Index (PI) (06-11 18:32:36) elapsed: 26.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/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/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_tss.bed` (68924,68925)
Command completed. Elapsed time: 0:00:02. Running peak memory: 4.586GB.
PID: 68924; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 68925; Command: bedtools; Return code: 0; Memory used: 0.093GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/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/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed` (68932,68933)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.586GB.
PID: 68932; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 68933; Command: bedtools; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/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/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSS_density.bed` (68936,68937,68938,68939)
Command completed. Elapsed time: 0:00:20. Running peak memory: 4.586GB.
PID: 68936; Command: bedtools; Return code: 0; Memory used: 0.056GB
PID: 68938; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 68937; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 68939; Command: sort; Return code: 0; Memory used: 0.003GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_gene_body_density.bed` (68995,68996,68997)
Command completed. Elapsed time: 0:00:27. Running peak memory: 4.586GB.
PID: 68996; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 68995; Command: bedtools; Return code: 0; Memory used: 0.137GB
PID: 68997; Command: sort; Return code: 0; Memory used: 0.003GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_pause_index.bed`
awk: cmd. line:1: { 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}}
awk: cmd. line:1: ^ syntax error
awk: cmd. line:1: { 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}}
awk: cmd. line:1: ^ syntax error
> `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/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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/HelaS3_GRO-seq/QC_hg38/tmp0l2qc6_9` (69034,69035,69036)
Got SIGTERM. Failing gracefully... (06-11 18:55:15) elapsed: 1359.0 _TIME_
Child process 69034 (join) terminated after 0 sec.
Setting dynamic recover file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/recover.lock.QC_hg38__HelaS3_GRO-seq_pause_index.bed
### Pipeline failed at: (06-11 18:55:15) elapsed: 0.0 _TIME_
Total time: 1:23:16
Failure reason: SIGTERM
Pipeline aborted.
### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name HelaS3_GRO-seq --genome hg38 --input /project/shefflab/data//sra_fastq/SRR1693611.fastq.gz /project/shefflab/data//sra_fastq/SRR1693612.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol GRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-ba27-12
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/
* Pipeline started at: (06-11 19:10:15) elapsed: 0.0 _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, 16373 insertions(+), 3522 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//sra_fastq/SRR1693611.fastq.gz', '/project/shefflab/data//sra_fastq/SRR1693612.fastq.gz']`
* `input2`: `None`
* `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`: `False`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `GRO`
* `recover`: `True`
* `sample_name`: `HelaS3_GRO-seq`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `SINGLE`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `0`
* `verbosity`: `None`
----------------------------------------
Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//sra_fastq/SRR1693611.fastq.gz
> `File_mb` 3550.33 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected GRO input
### Merge/link and fastq conversion: (06-11 19:10:15) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz'
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz']
### FASTQ processing: (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/processed_R1.flag`
### Plot adapter insertion distribution (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_adapter_insertion_distribution.pdf`
> `Adapter insertion distribution` cutadapt/HelaS3_GRO-seq_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/HelaS3_GRO-seq_R1_adapter_insertion_distribution.png PEPPRO _OBJ_
### Prealignments (06-11 19:10:15) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-11 19:10:15) elapsed: 0.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/prealignments/HelaS3_GRO-seq_human_rDNA_unmap.fq
### Map to genome (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam`
### Compress all unmapped read files (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/prealignments/HelaS3_GRO-seq_human_rDNA_unmap.fq.gz`
### Calculate NRF, PBC1, and PBC2 (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam.bai`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_bamQC.tsv`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_unmap.bam`
### Split BAM by strand (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam`
### Calculate TSS enrichment (06-11 19:10:15) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSSenrichment.pdf`
> `TSS enrichment` QC_hg38/HelaS3_GRO-seq_TSSenrichment.pdf TSS enrichment QC_hg38/HelaS3_GRO-seq_TSSenrichment.png PEPPRO _OBJ_
### Calculate Pause Index (PI) (06-11 19:10:15) elapsed: 0.0 _TIME_
Missing stat 'Pause_index'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_tss.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSS_density.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_gene_body_density.bed`
Found lock file: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/lock.QC_hg38__HelaS3_GRO-seq_pause_index.bed
Overwriting target...
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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/HelaS3_GRO-seq/QC_hg38/tmpv8eq039_` (115692,115693,115694)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.006GB.
PID: 115692; Command: join; Return code: 0; Memory used: 0.001GB
PID: 115694; Command: env; Return code: 0; Memory used: 0.006GB
PID: 115693; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/tmpv8eq039_ | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}`
/bin/sh: -c: line 0: unexpected EOF while looking for matching `''
/bin/sh: -c: line 1: syntax error: unexpected end of file
### Pipeline failed at: (06-11 19:10:16) elapsed: 0.0 _TIME_
Total time: 0:00:01
Failure reason: Command 'awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/tmpv8eq039_ | sort -n | awk 'BEGIN{i=0} {s[i]=$1; i++;} END{print s[int(NR*0.5-0.5)]}' returned non-zero exit status 1.
### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name HelaS3_GRO-seq --genome hg38 --input /project/shefflab/data//sra_fastq/SRR1693611.fastq.gz /project/shefflab/data//sra_fastq/SRR1693612.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol GRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-aj37-18c0
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/
* Pipeline started at: (06-14 21:14:10) elapsed: 9.0 _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, 16373 insertions(+), 3522 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//sra_fastq/SRR1693611.fastq.gz', '/project/shefflab/data//sra_fastq/SRR1693612.fastq.gz']`
* `input2`: `None`
* `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`: `False`
* `pre_name`: `None`
* `prealignments`: `['human_rDNA']`
* `prioritize`: `False`
* `protocol`: `GRO`
* `recover`: `True`
* `sample_name`: `HelaS3_GRO-seq`
* `scale`: `True`
* `search_file`: `None`
* `silent`: `False`
* `single_or_paired`: `SINGLE`
* `sob`: `False`
* `testmode`: `False`
* `trimmer`: `seqtk`
* `umi_len`: `0`
* `verbosity`: `None`
----------------------------------------
Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/PEPPRO_failed.flag'
Local input file: /project/shefflab/data//sra_fastq/SRR1693611.fastq.gz
> `File_mb` 3550.33 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected GRO input
### Merge/link and fastq conversion: (06-14 21:14:11) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz`
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz'
Found .fastq.gz file
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/HelaS3_GRO-seq_R1.fastq`
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/HelaS3_GRO-seq.merged.fastq.gz']
### FASTQ processing: (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/fastq/processed_R1.flag`
### Plot adapter insertion distribution (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/cutadapt/HelaS3_GRO-seq_R1_adapter_insertion_distribution.pdf`
> `Adapter insertion distribution` cutadapt/HelaS3_GRO-seq_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/HelaS3_GRO-seq_R1_adapter_insertion_distribution.png PEPPRO _OBJ_
### Prealignments (06-14 21:14:11) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-14 21:14:11) elapsed: 0.0 _TIME_
No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/prealignments/HelaS3_GRO-seq_human_rDNA_unmap.fq
### Map to genome (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam`
### Compress all unmapped read files (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/prealignments/HelaS3_GRO-seq_human_rDNA_unmap.fq.gz`
### Calculate NRF, PBC1, and PBC2 (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam.bai`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_bamQC.tsv`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_unmap.bam`
### Split BAM by strand (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam`
### Calculate TSS enrichment (06-14 21:14:11) elapsed: 0.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSSenrichment.pdf`
> `TSS enrichment` QC_hg38/HelaS3_GRO-seq_TSSenrichment.pdf TSS enrichment QC_hg38/HelaS3_GRO-seq_TSSenrichment.png PEPPRO _OBJ_
### Calculate Pause Index (PI) (06-14 21:14:11) elapsed: 0.0 _TIME_
Missing stat 'Pause_index'
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_tss.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_ensembl_gene_body.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSS_density.bed`
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_gene_body_density.bed`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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/HelaS3_GRO-seq/QC_hg38/tmpdxowb6b2` (428182,428190,428202)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.005GB.
PID: 428182; Command: join; Return code: 0; Memory used: 0.001GB
PID: 428202; Command: env; Return code: 0; Memory used: 0.005GB
PID: 428190; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/tmpdxowb6b2 | 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/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.0143043) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/tmpdxowb6b2 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_pause_index.bed` (428270)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.005GB.
PID: 428270; Command: awk; Return code: 0; Memory used: 0.002GB
> `sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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` 4.92 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_pause_index.bed` (428309)
Pause index plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.279GB.
PID: 428309; Command: Rscript; Return code: 0; Memory used: 0.279GB
> `Pause index` QC_hg38/HelaS3_GRO-seq_pause_index.pdf Pause index QC_hg38/HelaS3_GRO-seq_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_pause_index.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_pause_index.bed` (429785)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.279GB.
PID: 429785; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-14 21:14:18) elapsed: 6.0 _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/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam`
14866164 5457524
> `Plus_FRiP` 0.37 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/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam`
14866164 4922927
> `Minus_FRiP` 0.33 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/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/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_gene_sort.bed` (430831,430832)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.279GB.
PID: 430831; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 430832; Command: bedtools; Return code: 0; Memory used: 0.005GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_gene_coverage.bed` (430834)
Command completed. Elapsed time: 0:00:24. Running peak memory: 0.279GB.
PID: 430834; Command: bedtools; Return code: 0; Memory used: 0.104GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/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/HelaS3_GRO-seq/raw/hg38_annotations.bed.gz` (431057)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.279GB.
PID: 431057; Command: ln; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/hg38_annotations.bed` (431058)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.279GB.
PID: 431058; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-14 21:15:07) elapsed: 49.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/raw/hg38_annotations.bed` (431067)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.279GB.
PID: 431067; Command: awk; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Enhancer_sort.bed` (431070,431071,431072,431073)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.279GB.
PID: 431070; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431071; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 431073; Command: bedtools; Return code: 0; Memory used: 0.045GB
PID: 431072; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Enhancer_plus_coverage.bed` (431075)
Command completed. Elapsed time: 0:00:09. Running peak memory: 0.279GB.
PID: 431075; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Enhancer_minus_coverage.bed` (431110)
Command completed. Elapsed time: 0:00:08. Running peak memory: 0.279GB.
PID: 431110; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_sort.bed` (431123,431124,431125,431126)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.279GB.
PID: 431123; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431124; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 431126; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 431125; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_plus_coverage.bed` (431128)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.279GB.
PID: 431128; Command: bedtools; Return code: 0; Memory used: 0.061GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_minus_coverage.bed` (431141)
Command completed. Elapsed time: 0:00:08. Running peak memory: 0.279GB.
PID: 431141; Command: bedtools; Return code: 0; Memory used: 0.067GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_Flanking_Region"` (431156)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.279GB.
PID: 431156; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed` (431157,431158,431159,431160)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.279GB.
PID: 431157; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431159; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 431158; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 431160; Command: bedtools; Return code: 0; Memory used: 0.013GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_Flanking_Region_plus_coverage.bed` (431163)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.279GB.
PID: 431163; Command: bedtools; Return code: 0; Memory used: 0.015GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_Flanking_Region_minus_coverage.bed` (431180)
Command completed. Elapsed time: 0:00:08. Running peak memory: 0.279GB.
PID: 431180; Command: bedtools; Return code: 0; Memory used: 0.011GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/5_UTR"` (431212)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.279GB.
PID: 431212; Command: mv; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/5_UTR_sort.bed` (431213,431214,431215,431216)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.279GB.
PID: 431213; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431214; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 431216; Command: bedtools; Return code: 0; Memory used: 0.03GB
PID: 431215; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_5_UTR_plus_coverage.bed` (431219)
Command completed. Elapsed time: 0:00:09. Running peak memory: 0.279GB.
PID: 431219; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_5_UTR_minus_coverage.bed` (431231)
Command completed. Elapsed time: 0:00:08. Running peak memory: 0.279GB.
PID: 431231; Command: bedtools; Return code: 0; Memory used: 0.008GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/3_UTR"` (431240)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.279GB.
PID: 431240; Command: mv; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/3_UTR_sort.bed` (431241,431242,431243,431244)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.279GB.
PID: 431241; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431242; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 431244; Command: bedtools; Return code: 0; Memory used: 0.035GB
PID: 431243; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_3_UTR_plus_coverage.bed` (431246)
Command completed. Elapsed time: 0:00:09. Running peak memory: 0.279GB.
PID: 431246; Command: bedtools; Return code: 0; Memory used: 0.016GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_3_UTR_minus_coverage.bed` (431264)
Command completed. Elapsed time: 0:00:08. Running peak memory: 0.279GB.
PID: 431264; Command: bedtools; Return code: 0; Memory used: 0.019GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Exon_sort.bed` (431275,431276,431277,431278)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.279GB.
PID: 431275; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 431276; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 431278; Command: bedtools; Return code: 0; Memory used: 0.159GB
PID: 431277; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Exon_plus_coverage.bed` (431282)
Command completed. Elapsed time: 0:00:12. Running peak memory: 0.279GB.
PID: 431282; Command: bedtools; Return code: 0; Memory used: 0.037GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Exon_minus_coverage.bed` (431333)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.279GB.
PID: 431333; Command: bedtools; Return code: 0; Memory used: 0.057GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Intron_sort.bed` (436224,436225,436226,436227)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.279GB.
PID: 436224; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 436226; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 436225; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 436227; Command: bedtools; Return code: 0; Memory used: 0.079GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Intron_plus_coverage.bed` (437383)
Command completed. Elapsed time: 0:00:12. Running peak memory: 0.279GB.
PID: 437383; Command: bedtools; Return code: 0; Memory used: 0.04GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Intron_minus_coverage.bed` (453287)
Command completed. Elapsed time: 0:00:11. Running peak memory: 0.279GB.
PID: 453287; Command: bedtools; Return code: 0; Memory used: 0.05GB
### Plot cFRiF/FRiF (06-14 21:17:29) elapsed: 142.0 _TIME_
> `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s HelaS3_GRO-seq -z 3099922541 -n 7116450 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Intron_plus_coverage.bed` (11157)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:32. Running peak memory: 0.475GB.
PID: 11157; Command: Rscript; Return code: 0; Memory used: 0.475GB
> `cFRiF` QC_hg38/HelaS3_GRO-seq_cFRiF.pdf cFRiF QC_hg38/HelaS3_GRO-seq_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s HelaS3_GRO-seq -z 3099922541 -n 7116450 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_Intron_plus_coverage.bed` (22651)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:25. Running peak memory: 0.513GB.
PID: 22651; Command: Rscript; Return code: 0; Memory used: 0.513GB
> `FRiF` QC_hg38/HelaS3_GRO-seq_FRiF.pdf FRiF QC_hg38/HelaS3_GRO-seq_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-14 21:18:27) elapsed: 58.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/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/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_exons_sort.bed` (44531,44533)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.513GB.
PID: 44533; Command: bedtools; Return code: 0; Memory used: 0.093GB
PID: 44531; Command: grep; Return code: 0; Memory used: 0.004GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/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/HelaS3_GRO-seq/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_introns_sort.bed` (50607,50620,50621)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.513GB.
PID: 50607; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 50621; Command: bedtools; Return code: 0; Memory used: 0.003GB
PID: 50620; Command: bedtools; Return code: 0; Memory used: 0.034GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_exons_coverage.bed` (55318)
Command completed. Elapsed time: 0:00:19. Running peak memory: 0.513GB.
PID: 55318; Command: bedtools; Return code: 0; Memory used: 0.397GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_introns_coverage.bed` (61248)
Command completed. Elapsed time: 0:00:19. Running peak memory: 0.513GB.
PID: 61248; Command: bedtools; Return code: 0; Memory used: 0.091GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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]/14.866164)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_exons_rpkm.bed` (61372,61373,61374)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.513GB.
PID: 61372; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 61374; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 61373; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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]/14.866164)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_introns_rpkm.bed` (61376,61377,61378)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.513GB.
PID: 61376; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 61378; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 61377; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_exon_intron_ratios.bed` (61381,61382,61383)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.513GB.
PID: 61381; Command: join; Return code: 0; Memory used: 0.001GB
PID: 61383; Command: sort; Return code: 0; Memory used: 0.005GB
PID: 61382; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_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` 3.22 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_mRNA_contamination.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_exon_intron_ratios.bed --annotate` (61389)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:04. Running peak memory: 0.513GB.
PID: 61389; Command: Rscript; Return code: 0; Memory used: 0.317GB
> `mRNA contamination` QC_hg38/HelaS3_GRO-seq_mRNA_contamination.pdf mRNA contamination QC_hg38/HelaS3_GRO-seq_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_exon_intron_ratios.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/QC_hg38/HelaS3_GRO-seq_exon_intron_ratios.bed` (61409)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.513GB.
PID: 61409; Command: pigz; Return code: 0; Memory used: 0.005GB
### Produce bigWig files (06-14 21:19:21) elapsed: 54.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam` (61417)
Command completed. Elapsed time: 0:00:05. Running peak memory: 0.513GB.
PID: 61417; Command: samtools; Return code: 0; Memory used: 0.009GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_plus_smooth_body_0-mer.bw -p 8 --variable-step --scale 14866164.0` (61423)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_plus.bam'
Temporary files will be stored in: 'tmp_HelaS3_GRO-seq_plus_cuttrace_dqxcnk7g'
Processing with 4 cores...
Discarding 134 chunk(s) of reads: ['chrM', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270714v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr14_GL000225v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_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_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_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_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', '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_GL000220v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrEBV']
Keeping 61 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_KI270712v1_random', 'chr1_KI270713v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270725v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270467v1', 'chrUn_KI270438v1', 'chrUn_KI270333v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000224v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270755v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1']
Reduce step (merge files)...
Merging 61 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_plus_exact_body_0-mer.bw'
Merging 61 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:05:23. Running peak memory: 3.503GB.
PID: 61423; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.503GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam` (151408)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.503GB.
PID: 151408; Command: samtools; Return code: 0; Memory used: 0.01GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_minus_smooth_body_0-mer.bw -p 8 --variable-step --scale 14866164.0` (151418)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/aligned_hg38/HelaS3_GRO-seq_minus.bam'
Temporary files will be stored in: 'tmp_HelaS3_GRO-seq_minus_cuttrace_a8m5gu0r'
Processing with 4 cores...
stdin is empty of data
Discarding 135 chunk(s) of reads: ['chrM', 'chr1_KI270708v1_random', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_KI270722v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270726v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270735v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', '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_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_GL000216v2', 'chrEBV']
Keeping 60 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_GL000194v1_random', 'chr14_KI270725v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270438v1', 'chrUn_KI270538v1', 'chrUn_KI270582v1', 'chrUn_KI270330v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000213v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270742v1', 'chrUn_GL000218v1']
Reduce step (merge files)...
Merging 60 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_minus_exact_body_0-mer.bw'
Merging 60 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HelaS3_GRO-seq/signal_hg38/HelaS3_GRO-seq_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:05:18. Running peak memory: 3.524GB.
PID: 151418; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.524GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:16:11
* Total elapsed time (all runs): 1:08:54
* Peak memory (this run): 3.524 GB
* Pipeline completed time: 2020-06-14 21:30:12