### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_PRO-seq_50 --genome hg38 --input /project/shefflab/data//guertin/fastq/K562_PRO_50pct.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 16 -M 16000 --protocol PRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R`
* Compute host: udc-aw29-26b
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/
* Pipeline started at: (06-15 07:11:05) elapsed: 3.0 _TIME_
### Version log:
* Python version: 3.6.6
* Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper`
* Pypiper version: 0.12.1
* Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines`
* Pipeline version: 0.9.8
* Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10
* Pipeline branch: * master
* Pipeline date: 2020-06-09 11:36:49 -0400
* Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-)
### Arguments passed to pipeline:
* `TSS_name`: `None`
* `adapter`: `cutadapt`
* `anno_name`: `None`
* `complexity`: `False`
* `config_file`: `peppro.yaml`
* `cores`: `16`
* `coverage`: `False`
* `dedup`: `seqkit`
* `dirty`: `True`
* `ensembl_gene_body`: `None`
* `ensembl_tss`: `None`
* `exon_name`: `None`
* `force_follow`: `False`
* `genome_assembly`: `hg38`
* `input`: `['/project/shefflab/data//guertin/fastq/K562_PRO_50pct.fastq.gz']`
* `input2`: `None`
* `intron_name`: `None`
* `keep`: `False`
* `logdev`: `False`
* `max_len`: `-1`
* `mem`: `16000`
* `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`: `PRO`
* `recover`: `True`
* `sample_name`: `K562_PRO-seq_50`
* `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//guertin/fastq/K562_PRO_50pct.fastq.gz
> `File_mb` 18213.9 PEPPRO _RES_
> `Read_type` SINGLE PEPPRO _RES_
> `Genome` hg38 PEPPRO _RES_
Detected PRO input
### Merge/link and fastq conversion: (06-15 07:11:05) elapsed: 1.0 _TIME_
Number of input file sets: 1
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/raw/K562_PRO-seq_50.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/K562_PRO_50pct.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/raw/K562_PRO-seq_50.fastq.gz` (208284)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 208284; Command: ln; Return code: 0; Memory used: 0.0GB
Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/raw/K562_PRO-seq_50.fastq.gz'
Found .fastq.gz file
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1.fastq`
> `pigz -f -p 16 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/raw/K562_PRO-seq_50.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1.fastq` (208287)
Command completed. Elapsed time: 0:09:50. Running peak memory: 0.003GB.
PID: 208287; Command: pigz; Return code: 0; Memory used: 0.003GB
> `Raw_reads` 248316549 PEPPRO _RES_
> `Fastq_reads` 248316549 PEPPRO _RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/raw/K562_PRO-seq_50.fastq.gz']
### FASTQ processing: (06-15 07:32:58) elapsed: 1313.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1_processed.fastq`
> `(cutadapt -j 16 -m 2 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_R1_cutadapt.txt` (210371)
Command completed. Elapsed time: 0:11:40. Running peak memory: 6.72GB.
PID: 210371; Command: cutadapt; Return code: 0; Memory used: 6.72GB
> `seqtk trimfq -b 0 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1_noadap.fastq | seqtk seq -L 2 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1_processed.fastq` (211485,211486)
Command completed. Elapsed time: 0:06:14. Running peak memory: 6.72GB.
PID: 211486; Command: seqtk; Return code: 0; Memory used: 0.002GB
PID: 211485; Command: seqtk; Return code: 0; Memory used: 0.001GB
> `grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 211550349.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_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/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 6217636.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 2.5039 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastqc/K562_PRO-seq_50_R1_processed_fastqc.html`
> `echo '### Calculate the number of trimmed reads'` (212485)
### Calculate the number of trimmed reads
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.72GB.
PID: 212485; Command: echo; Return code: 0; Memory used: 0.0GB
Evaluating read trimming
> `Trimmed_reads` 242098913 PEPPRO _RES_
> `Trim_loss_rate` 2.5 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1_processed.fastq` (212735)
Started analysis of K562_PRO-seq_50_R1_processed.fastq
Approx 5% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 10% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 15% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 20% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 25% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 30% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 35% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 40% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 45% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 50% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 55% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 60% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 65% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 70% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 75% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 80% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 85% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 90% complete for K562_PRO-seq_50_R1_processed.fastq
Approx 95% complete for K562_PRO-seq_50_R1_processed.fastq
Analysis complete for K562_PRO-seq_50_R1_processed.fastq
Command completed. Elapsed time: 0:13:13. Running peak memory: 6.72GB.
PID: 212735; Command: fastqc; Return code: 0; Memory used: 0.252GB
> `FastQC report r1` fastqc/K562_PRO-seq_50_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/processed_R1.flag` (213985)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.72GB.
PID: 213985; Command: touch; Return code: 0; Memory used: 0.002GB
### Plot adapter insertion distribution (06-15 08:09:08) elapsed: 2170.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_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/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_R1_cutadapt.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/cutadapt` (213991)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.72GB.
PID: 213991; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `Adapter insertion distribution` cutadapt/K562_PRO-seq_50_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_PRO-seq_50_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/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_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` 34 PEPPRO _RES_
Missing stat 'Degradation_ratio'
### Calculating degradation ratio (06-15 08:09:13) elapsed: 5.0 _TIME_
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_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/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_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/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_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/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_R1_cutadapt.txt | awk '{ if ($1 == 40) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk '/count/,0' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/cutadapt/K562_PRO-seq_50_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 <= 20 && $1 >= 10){degradedSum += $2}; ($1 >= 30 && $1 <= 40){intactSum += $2} END {if (intactSum < 1) {intactSum = 1} print degradedSum/intactSum}'`
> `Degradation_ratio` 0.2313 PEPPRO _RES_
### Prealignments (06-15 08:09:13) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-15 08:09:13) elapsed: 0.0 _TIME_
> `(bowtie2 -p 16 -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 K562_PRO-seq_50 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/fastq/K562_PRO-seq_50_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/prealignments/K562_PRO-seq_50_human_rDNA_unmap.fq 2>&1 > /dev/null)`
Missing stat 'Aligned_reads_human_rDNA'
242098913 reads; of these:
242098913 (100.00%) were unpaired; of these:
219756437 (90.77%) aligned 0 times
22342476 (9.23%) aligned exactly 1 time
0 (0.00%) aligned >1 times
9.23% overall alignment rate
> `Aligned_reads_human_rDNA` 22342476.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 9.23 PEPPRO _RES_
### Map to genome (06-15 08:45:23) elapsed: 2169.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam`
> `bowtie2 -p 16 --very-sensitive --rg-id K562_PRO-seq_50 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/prealignments/K562_PRO-seq_50_human_rDNA_unmap.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/tmph50h2hb_ -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_temp.bam` (219931,220017,220018)
219756437 reads; of these:
219756437 (100.00%) were unpaired; of these:
2697646 (1.23%) aligned 0 times
164092013 (74.67%) aligned exactly 1 time
52966778 (24.10%) aligned >1 times
98.77% overall alignment rate
[bam_sort_core] merging from 70 files and 1 in-memory blocks...
Command completed. Elapsed time: 2:07:48. Running peak memory: 6.72GB.
PID: 220017; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 219931; Command: bowtie2; Return code: 0; Memory used: 3.845GB
PID: 220018; Command: samtools; Return code: 0; Memory used: 0.9GB
> `samtools view -q 10 -b -@ 16 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam` (237040)
Command completed. Elapsed time: 0:06:04. Running peak memory: 6.72GB.
PID: 237040; Command: samtools; Return code: 0; Memory used: 0.026GB
> `samtools depth -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 217058791 PEPPRO _RES_
> `QC_filtered_reads` 23375045 PEPPRO _RES_
> `Aligned_reads` 193683746 PEPPRO _RES_
> `Alignment_rate` 80.0 PEPPRO _RES_
> `Total_efficiency` 78.0 PEPPRO _RES_
> `Read_depth` 16.03 PEPPRO _RES_
### Compress all unmapped read files (06-15 11:39:29) elapsed: 10447.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/prealignments/K562_PRO-seq_50_human_rDNA_unmap.fq.gz`
> `pigz -f -p 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/prealignments/K562_PRO-seq_50_human_rDNA_unmap.fq` (241954)
Command completed. Elapsed time: 0:05:30. Running peak memory: 6.72GB.
PID: 241954; Command: pigz; Return code: 0; Memory used: 0.014GB
Missing stat 'Mitochondrial_reads'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_temp.bam` (242600)
Command completed. Elapsed time: 0:03:22. Running peak memory: 6.72GB.
PID: 242600; Command: samtools; Return code: 0; Memory used: 0.022GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 4576683 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam` (243016)
Command completed. Elapsed time: 0:02:56. Running peak memory: 6.72GB.
PID: 243016; Command: samtools; Return code: 0; Memory used: 0.022GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_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/K562_PRO-seq_50/aligned_hg38/chr_sizes.bed` (270996,270997,270998,270999)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.72GB.
PID: 270997; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 270999; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 270996; Command: samtools; Return code: 0; Memory used: 0.01GB
PID: 270998; Command: awk; Return code: 0; Memory used: 0.0GB
> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/chr_sizes.bed -b -@ 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_noMT.bam` (271001)
Command completed. Elapsed time: 0:03:37. Running peak memory: 6.72GB.
PID: 271001; Command: samtools; Return code: 0; Memory used: 0.023GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam` (279626)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.72GB.
PID: 279626; Command: mv; Return code: 0; Memory used: 0.001GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam` (280008)
Command completed. Elapsed time: 0:02:56. Running peak memory: 6.72GB.
PID: 280008; Command: samtools; Return code: 0; Memory used: 0.022GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-`
> `Maximum_read_length` 100 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 (06-15 12:06:45) elapsed: 1635.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam.bai`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_bamQC.tsv`
> `/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam -c 16 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_bamQC.tsv` (338745)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/tmp_K562_PRO-seq_50_sort__n9_22y7'
Processing with 16 cores...
Discarding 86 chunk(s) of reads: ['chrM', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270581v1', 'chrUn_KI270593v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', '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_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1']
Keeping 109 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270310v1', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270515v1', 'chrUn_KI270538v1', 'chrUn_KI270583v1', 'chrUn_KI270580v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Command completed. Elapsed time: 0:03:15. Running peak memory: 7.423GB.
PID: 338745; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 7.423GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_bamQC.tsv`
> `NRF` 0.47 PEPPRO _RES_
> `PBC1` 0.7 PEPPRO _RES_
> `PBC2` 4.99 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_unmap.bam`
> `samtools view -b -@ 16 -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_unmap.bam` (382983)
Command completed. Elapsed time: 0:00:38. Running peak memory: 7.423GB.
PID: 382983; Command: samtools; Return code: 0; Memory used: 0.011GB
> `samtools view -c -f 4 -@ 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_temp.bam`
> `Unmapped_reads` 2697646 PEPPRO _RES_
### Split BAM by strand (06-15 12:11:11) elapsed: 267.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam` (383351)
Command completed. Elapsed time: 0:14:01. Running peak memory: 7.423GB.
PID: 383351; Command: samtools; Return code: 0; Memory used: 0.006GB
> `samtools view -bh -f 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam` (51589)
Command completed. Elapsed time: 0:13:29. Running peak memory: 7.423GB.
PID: 51589; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-15 12:38:41) elapsed: 1649.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (172739)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 172739; Command: sed; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_plus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/plus_TSS.tsv -p ends -c 16 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_plus_TssEnrichment.txt` (173003)
Command completed. Elapsed time: 0:00:25. Running peak memory: 7.423GB.
PID: 173003; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 1.063GB
> `TSS_coding_score` 13.9 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_minus_TssEnrichment.txt`
> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/minus_TSS.tsv -p ends -c 16 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_minus_TssEnrichment.txt` (181856)
Command completed. Elapsed time: 0:00:21. Running peak memory: 7.423GB.
PID: 181856; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 1.049GB
> `TSS_non-coding_score` 5.8 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_TSSenrichment.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_minus_TssEnrichment.txt` (187364)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_minus_TssEnrichment.txt
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
TSS enrichment plot completed!
Command completed. Elapsed time: 0:00:06. Running peak memory: 7.423GB.
PID: 187364; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `TSS enrichment` QC_hg38/K562_PRO-seq_50_TSSenrichment.pdf TSS enrichment QC_hg38/K562_PRO-seq_50_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_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/K562_PRO-seq_50/QC_hg38/chr_order.txt` (187419,187420,187421,187422)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 187419; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 187421; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 187420; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 187422; Command: awk; Return code: 0; Memory used: 0.0GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_keep.txt` (187424)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 187424; Command: cut; Return code: 0; Memory used: 0.0GB
### Calculate Pause Index (PI) (06-15 12:39:33) elapsed: 53.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/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/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_ensembl_tss.bed` (187426,187427)
Command completed. Elapsed time: 0:00:02. Running peak memory: 7.423GB.
PID: 187426; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 187427; Command: bedtools; Return code: 0; Memory used: 0.095GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/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/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_ensembl_gene_body.bed` (187432,187433)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 187432; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 187433; Command: bedtools; Return code: 0; Memory used: 0.005GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/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/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_TSS_density.bed` (187435,187436,187437,187438)
Command completed. Elapsed time: 0:04:10. Running peak memory: 7.423GB.
PID: 187435; Command: bedtools; Return code: 0; Memory used: 0.055GB
PID: 187437; Command: sort; Return code: 0; Memory used: 0.014GB
PID: 187436; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 187438; Command: sort; Return code: 0; Memory used: 0.003GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_gene_body_density.bed` (194172,194173,194175)
Command completed. Elapsed time: 0:06:38. Running peak memory: 7.423GB.
PID: 194175; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 194172; Command: bedtools; Return code: 0; Memory used: 0.524GB
PID: 194173; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_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/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_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/K562_PRO-seq_50/QC_hg38/tmpv1edhois` (195123,195124,195125)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 195123; Command: join; Return code: 0; Memory used: 0.001GB
PID: 195125; Command: env; Return code: 0; Memory used: 0.005GB
PID: 195124; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/tmpv1edhois | 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/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.119401) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/tmpv1edhois > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_pause_index.bed` (195131)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 195131; Command: awk; Return code: 0; Memory used: 0.002GB
> `sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_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` 10.88 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_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/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_pause_index.bed` (195136)
Pause index plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 7.423GB.
PID: 195136; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `Pause index` QC_hg38/K562_PRO-seq_50_pause_index.pdf Pause index QC_hg38/K562_PRO-seq_50_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_pause_index.bed.gz`
> `pigz -f -p 16 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_pause_index.bed` (195160)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 195160; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-15 12:50:29) elapsed: 656.0 _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/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam`
193683746 69078220
> `Plus_FRiP` 0.36 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/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam`
193683746 65709582
> `Minus_FRiP` 0.34 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/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/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_gene_sort.bed` (195667,195668)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.423GB.
PID: 195667; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 195668; 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/K562_PRO-seq_50/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_gene_coverage.bed` (195670)
Command completed. Elapsed time: 0:06:33. Running peak memory: 7.423GB.
PID: 195670; Command: bedtools; Return code: 0; Memory used: 0.52GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/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/K562_PRO-seq_50/raw/hg38_annotations.bed.gz` (196281)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 196281; Command: ln; Return code: 0; Memory used: 0.002GB
> `pigz -f -p 16 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/raw/hg38_annotations.bed` (196287)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 196287; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 13:02:37) elapsed: 728.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/raw/hg38_annotations.bed` (196296)
Command completed. Elapsed time: 0:00:02. Running peak memory: 7.423GB.
PID: 196296; Command: awk; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Enhancer_sort.bed` (196300,196301,196302,196303)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.423GB.
PID: 196300; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 196301; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 196303; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 196302; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Enhancer_plus_coverage.bed` (196306)
Command completed. Elapsed time: 0:02:07. Running peak memory: 7.423GB.
PID: 196306; Command: bedtools; Return code: 0; Memory used: 0.022GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Enhancer_minus_coverage.bed` (196423)
Command completed. Elapsed time: 0:02:00. Running peak memory: 7.423GB.
PID: 196423; Command: bedtools; Return code: 0; Memory used: 0.038GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_sort.bed` (196718,196719,196720,196721)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 196718; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 196719; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 196721; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 196720; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_plus_coverage.bed` (196723)
Command completed. Elapsed time: 0:02:12. Running peak memory: 7.423GB.
PID: 196723; Command: bedtools; Return code: 0; Memory used: 0.284GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_minus_coverage.bed` (196875)
Command completed. Elapsed time: 0:02:10. Running peak memory: 7.423GB.
PID: 196875; Command: bedtools; Return code: 0; Memory used: 0.239GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_Flanking_Region"` (197225)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 197225; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_Flanking_Region_sort.bed` (197226,197227,197228,197229)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.423GB.
PID: 197226; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 197228; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 197227; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 197229; Command: bedtools; Return code: 0; Memory used: 0.01GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_Flanking_Region_plus_coverage.bed` (197232)
Command completed. Elapsed time: 0:02:06. Running peak memory: 7.423GB.
PID: 197232; Command: bedtools; Return code: 0; Memory used: 0.053GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_Flanking_Region_minus_coverage.bed` (199936)
Command completed. Elapsed time: 0:02:07. Running peak memory: 7.423GB.
PID: 199936; Command: bedtools; Return code: 0; Memory used: 0.086GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/5_UTR"` (201131)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 201131; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/5_UTR_sort.bed` (201132,201133,201134,201135)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.423GB.
PID: 201132; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 201133; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 201135; Command: bedtools; Return code: 0; Memory used: 0.01GB
PID: 201134; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_5_UTR_plus_coverage.bed` (201138)
Command completed. Elapsed time: 0:02:03. Running peak memory: 7.423GB.
PID: 201138; Command: bedtools; Return code: 0; Memory used: 0.042GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_5_UTR_minus_coverage.bed` (201246)
Command completed. Elapsed time: 0:01:59. Running peak memory: 7.423GB.
PID: 201246; Command: bedtools; Return code: 0; Memory used: 0.035GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/3_UTR"` (201351)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 201351; Command: mv; Return code: 0; Memory used: 0.002GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/3_UTR_sort.bed` (201352,201353,201354,201355)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.423GB.
PID: 201352; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 201353; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 201355; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 201354; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_3_UTR_plus_coverage.bed` (201358)
Command completed. Elapsed time: 0:02:07. Running peak memory: 7.423GB.
PID: 201358; Command: bedtools; Return code: 0; Memory used: 0.056GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_3_UTR_minus_coverage.bed` (201699)
Command completed. Elapsed time: 0:02:02. Running peak memory: 7.423GB.
PID: 201699; Command: bedtools; Return code: 0; Memory used: 0.084GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Exon_sort.bed` (201806,201807,201808,201809)
Command completed. Elapsed time: 0:00:03. Running peak memory: 7.423GB.
PID: 201806; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 201807; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 201809; Command: bedtools; Return code: 0; Memory used: 0.174GB
PID: 201808; Command: cut; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Exon_plus_coverage.bed` (201814)
Command completed. Elapsed time: 0:02:16. Running peak memory: 7.423GB.
PID: 201814; Command: bedtools; Return code: 0; Memory used: 0.239GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Exon_minus_coverage.bed` (202129)
Command completed. Elapsed time: 0:02:07. Running peak memory: 7.423GB.
PID: 202129; Command: bedtools; Return code: 0; Memory used: 0.097GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Intron_sort.bed` (202347,202348,202349,202350)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.423GB.
PID: 202347; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 202349; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 202348; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 202350; Command: bedtools; Return code: 0; Memory used: 0.083GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Intron_plus_coverage.bed` (202361)
Command completed. Elapsed time: 0:02:33. Running peak memory: 7.423GB.
PID: 202361; Command: bedtools; Return code: 0; Memory used: 0.228GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Intron_minus_coverage.bed` (202937)
Command completed. Elapsed time: 0:02:29. Running peak memory: 7.423GB.
PID: 202937; Command: bedtools; Return code: 0; Memory used: 0.222GB
### Plot cFRiF/FRiF (06-15 13:33:06) elapsed: 1830.0 _TIME_
> `samtools view -@ 16 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_PRO-seq_50 -z 3099922541 -n 96376229 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Intron_plus_coverage.bed` (203106)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:38. Running peak memory: 7.423GB.
PID: 203106; Command: Rscript; Return code: 0; Memory used: 0.461GB
> `cFRiF` QC_hg38/K562_PRO-seq_50_cFRiF.pdf cFRiF QC_hg38/K562_PRO-seq_50_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_PRO-seq_50 -z 3099922541 -n 96376229 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_Intron_plus_coverage.bed` (203154)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:26. Running peak memory: 7.423GB.
PID: 203154; Command: Rscript; Return code: 0; Memory used: 0.467GB
> `FRiF` QC_hg38/K562_PRO-seq_50_FRiF.pdf FRiF QC_hg38/K562_PRO-seq_50_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-15 13:34:26) elapsed: 80.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/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/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_exons_sort.bed` (203188,203189)
Command completed. Elapsed time: 0:00:05. Running peak memory: 7.423GB.
PID: 203189; Command: bedtools; Return code: 0; Memory used: 0.098GB
PID: 203188; Command: grep; Return code: 0; Memory used: 0.004GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/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/K562_PRO-seq_50/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_introns_sort.bed` (203195,203196,203197)
Command completed. Elapsed time: 0:00:05. Running peak memory: 7.423GB.
PID: 203195; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 203197; Command: bedtools; Return code: 0; Memory used: 0.003GB
PID: 203196; Command: bedtools; Return code: 0; Memory used: 0.037GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exons_coverage.bed` (203203)
Command completed. Elapsed time: 0:04:27. Running peak memory: 7.423GB.
PID: 203203; Command: bedtools; Return code: 0; Memory used: 0.15GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_introns_coverage.bed` (203723)
Command completed. Elapsed time: 0:05:20. Running peak memory: 7.423GB.
PID: 203723; Command: bedtools; Return code: 0; Memory used: 0.251GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_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]/193.683746)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exons_rpkm.bed` (204334,204335,204336)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.423GB.
PID: 204334; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 204336; Command: sort; Return code: 0; Memory used: 0.005GB
PID: 204335; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_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]/193.683746)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_introns_rpkm.bed` (204338,204339,204340)
Command completed. Elapsed time: 0:00:01. Running peak memory: 7.423GB.
PID: 204338; Command: awk; Return code: 0; Memory used: 0.008GB
PID: 204340; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 204339; Command: awk; Return code: 0; Memory used: 0.001GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_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/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exon_intron_ratios.bed` (204343,204344,204345)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 204343; Command: join; Return code: 0; Memory used: 0.001GB
PID: 204345; Command: sort; Return code: 0; Memory used: 0.006GB
PID: 204344; Command: awk; Return code: 0; Memory used: 0.001GB
> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exon_intron_ratios.bed | sort -n | awk ' { a[i++]=$1; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'`
> `mRNA_contamination` 1.37 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_mRNA_contamination.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exon_intron_ratios.bed --annotate` (204351)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 7.423GB.
PID: 204351; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `mRNA contamination` QC_hg38/K562_PRO-seq_50_mRNA_contamination.pdf mRNA contamination QC_hg38/K562_PRO-seq_50_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exon_intron_ratios.bed.gz`
> `pigz -f -p 16 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/QC_hg38/K562_PRO-seq_50_exon_intron_ratios.bed` (204374)
Command completed. Elapsed time: 0:00:00. Running peak memory: 7.423GB.
PID: 204374; Command: pigz; Return code: 0; Memory used: 0.003GB
### Produce bigWig files (06-15 13:44:30) elapsed: 604.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam` (204383)
Command completed. Elapsed time: 0:01:22. Running peak memory: 7.423GB.
PID: 204383; Command: samtools; Return code: 0; Memory used: 0.012GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_plus_smooth_body_0-mer.bw -p 10 --variable-step --tail-edge --scale 193683746.0` (204651)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_plus.bam'
Temporary files will be stored in: 'tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j'
Processing with 5 cores...
stdin is empty of data
stdin is empty of data
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr11.txt.bw to write: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr3.txt_smooth.bw to write: No such file or directory
tee: tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr4.txt_cuts.txt: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr11.txt_smooth.bw to write: No such file or directory
tee: tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr12.txt_cuts.txt: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr4.txt.bw to write: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr12.txt.bw to write: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr12.txt_smooth.bw to write: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr4.txt_smooth.bw to write: No such file or directory
tee: tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr5.txt_cuts.txt: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr5.txt.bw to write: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr5.txt_smooth.bw to write: No such file or directory
tee: tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr6.txt_cuts.txt: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr6.txt.bw to write: No such file or directory
mustOpen: Can't open tmp_K562_PRO-seq_50_plus_cuttrace_hliil13j/chr6.txt_smooth.bw to write: No such file or directory
Discarding 92 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_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_KI270581v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', '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_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1']
Keeping 103 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270538v1', 'chrUn_KI270580v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 103 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_plus_exact_body_0-mer.bw'
bigWigCat v 4 - merge non-overlapping bigWig files
directly into bigWig format
usage:
bigWigCat out.bw in1.bw in2.bw ...
Where in*.bw is in big wig format
and out.bw is the output indexed big wig file.
options:
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
Note: must use wigToBigWig -fixedSummaries -keepAllChromosomes (perhaps in parallel cluster jobs) to create the input files.
Note: By non-overlapping we mean the entire span of each file, from first data point to last data point, must not overlap with that of other files.
Merging 103 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_plus_smooth_body_0-mer.bw'
bigWigCat v 4 - merge non-overlapping bigWig files
directly into bigWig format
usage:
bigWigCat out.bw in1.bw in2.bw ...
Where in*.bw is in big wig format
and out.bw is the output indexed big wig file.
options:
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
Note: must use wigToBigWig -fixedSummaries -keepAllChromosomes (perhaps in parallel cluster jobs) to create the input files.
Note: By non-overlapping we mean the entire span of each file, from first data point to last data point, must not overlap with that of other files.
Command completed. Elapsed time: 0:07:57. Running peak memory: 7.423GB.
PID: 204651; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.644GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam` (206359)
Command completed. Elapsed time: 0:01:25. Running peak memory: 7.423GB.
PID: 206359; Command: samtools; Return code: 0; Memory used: 0.012GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_minus_smooth_body_0-mer.bw -p 10 --variable-step --tail-edge --scale 193683746.0` (206630)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/aligned_hg38/K562_PRO-seq_50_minus.bam'
Temporary files will be stored in: 'tmp_K562_PRO-seq_50_minus_cuttrace_6qrk7or_'
Processing with 5 cores...
stdin is empty of data
stdin is empty of data
Discarding 98 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr9_KI270717v1_random', 'chr14_KI270723v1_random', 'chr14_KI270725v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270593v1', '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_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1']
Keeping 97 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270710v1_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', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270310v1', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270515v1', 'chrUn_KI270538v1', 'chrUn_KI270583v1', 'chrUn_KI270589v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270448v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']
Reduce step (merge files)...
Merging 97 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_minus_exact_body_0-mer.bw'
Merging 97 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_PRO-seq_50/signal_hg38/K562_PRO-seq_50_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:08:49. Running peak memory: 7.423GB.
PID: 206630; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.583GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 6:53:02
* Total elapsed time (all runs): 8:51:51
* Peak memory (this run): 7.4232 GB
* Pipeline completed time: 2020-06-15 14:04:04