### Pipeline run code and environment: * Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_RNA-seq_90 --genome hg38 --input /project/shefflab/data//guertin/fastq/K562_90pctRNA.fastq.gz --single-or-paired SINGLE -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --protocol PRO --umi-len 0 --scale --prealignments human_rDNA --dirty -R` * Compute host: udc-ba26-32c1 * Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc * Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/ * Pipeline started at: (06-15 07:17:12) elapsed: 1.0 _TIME_ ### Version log: * Python version: 3.6.6 * Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines` * Pipeline version: 0.9.8 * Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10 * Pipeline branch: * master * Pipeline date: 2020-06-09 11:36:49 -0400 * Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-) ### Arguments passed to pipeline: * `TSS_name`: `None` * `adapter`: `cutadapt` * `anno_name`: `None` * `complexity`: `False` * `config_file`: `peppro.yaml` * `cores`: `12` * `coverage`: `False` * `dedup`: `seqkit` * `dirty`: `True` * `ensembl_gene_body`: `None` * `ensembl_tss`: `None` * `exon_name`: `None` * `force_follow`: `False` * `genome_assembly`: `hg38` * `input`: `['/project/shefflab/data//guertin/fastq/K562_90pctRNA.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`: `PRO` * `recover`: `True` * `sample_name`: `K562_RNA-seq_90` * `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_90pctRNA.fastq.gz > `File_mb` 5212.18 PEPPRO _RES_ > `Read_type` SINGLE PEPPRO _RES_ > `Genome` hg38 PEPPRO _RES_ Detected PRO input ### Merge/link and fastq conversion: (06-15 07:17:13) elapsed: 1.0 _TIME_ Number of input file sets: 1 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/K562_RNA-seq_90.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/K562_90pctRNA.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/K562_RNA-seq_90.fastq.gz` (341708)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.  
  PID: 341708;	Command: ln;	Return code: 0;	Memory used: 0.0GB

Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/K562_RNA-seq_90.fastq.gz'
Found .fastq.gz file
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1.fastq`  

> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/K562_RNA-seq_90.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1.fastq` (341709)

Command completed. Elapsed time: 0:02:30. Running peak memory: 0.002GB.  
  PID: 341709;	Command: pigz;	Return code: 0;	Memory used: 0.002GB


> `Raw_reads`	70000000	PEPPRO	_RES_

> `Fastq_reads`	70000000	PEPPRO	_RES_
['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/K562_RNA-seq_90.fastq.gz']

### FASTQ processing:  (06-15 07:21:13) elapsed: 241.0 _TIME_


> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1_processed.fastq`  

> `(cutadapt -j 12 -m 2 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/cutadapt/K562_RNA-seq_90_R1_cutadapt.txt` (342182)

Command completed. Elapsed time: 0:01:48. Running peak memory: 4.107GB.  
  PID: 342182;	Command: cutadapt;	Return code: 0;	Memory used: 4.107GB


> `seqtk trimfq -b 0 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1_noadap.fastq | seqtk seq -L 2 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1_processed.fastq` (342306,342307)

Command completed. Elapsed time: 0:01:41. Running peak memory: 4.107GB.  
  PID: 342306;	Command: seqtk;	Return code: 0;	Memory used: 0.001GB  
  PID: 342307;	Command: seqtk;	Return code: 0;	Memory used: 0.002GB


> `grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/cutadapt/K562_RNA-seq_90_R1_cutadapt.txt | awk '{print $(NF-1)}'`

> `Reads_with_adapter`	28335107.0	PEPPRO	_RES_

> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/cutadapt/K562_RNA-seq_90_R1_cutadapt.txt | awk '{print $(NF-1)}'`

> `awk '{sum+=$1*$2} END {printf "%.0f", sum}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/cutadapt/K562_RNA-seq_90_R1_cutadapt.txt`

> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1_short.fastq | awk '{print $1}'`

> `Uninformative_adapter_reads`	175101.0	PEPPRO	_RES_

> `Pct_uninformative_adapter_reads`	0.2501	PEPPRO	_RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastqc/K562_RNA-seq_90_R1_processed_fastqc.html`  

> `echo '### Calculate the number of trimmed reads'` (342647)
### Calculate the number of trimmed reads
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB. PID: 342647; Command: echo; Return code: 0; Memory used: 0.0GB Evaluating read trimming > `Trimmed_reads` 69824899 PEPPRO _RES_ > `Trim_loss_rate` 0.25 PEPPRO _RES_ Targetless command, running... > `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1_processed.fastq` (342674)
Started analysis of K562_RNA-seq_90_R1_processed.fastq
Approx 5% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 10% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 15% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 20% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 25% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 30% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 35% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 40% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 45% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 50% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 55% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 60% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 65% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 70% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 75% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 80% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 85% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 90% complete for K562_RNA-seq_90_R1_processed.fastq
Approx 95% complete for K562_RNA-seq_90_R1_processed.fastq
Analysis complete for K562_RNA-seq_90_R1_processed.fastq
Command completed. Elapsed time: 0:04:53. Running peak memory: 4.107GB. PID: 342674; Command: fastqc; Return code: 0; Memory used: 0.245GB > `FastQC report r1` fastqc/K562_RNA-seq_90_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/processed_R1.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/processed_R1.flag` (343188)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 343188;	Command: touch;	Return code: 0;	Memory used: 0.002GB


### Plot adapter insertion distribution (06-15 07:30:48) elapsed: 574.0 _TIME_

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/cutadapt/K562_RNA-seq_90_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_RNA-seq_90/cutadapt/K562_RNA-seq_90_R1_cutadapt.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/cutadapt` (343189)
Adapter insertion distribution plot completed!

Command completed. Elapsed time: 0:00:08. Running peak memory: 4.107GB. PID: 343189; Command: Rscript; Return code: 0; Memory used: 0.123GB > `Adapter insertion distribution` cutadapt/K562_RNA-seq_90_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_RNA-seq_90_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_RNA-seq_90/cutadapt/K562_RNA-seq_90_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 07:30:56) elapsed: 8.0 _TIME_ > `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/cutadapt/K562_RNA-seq_90_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_RNA-seq_90/cutadapt/K562_RNA-seq_90_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_RNA-seq_90/cutadapt/K562_RNA-seq_90_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_RNA-seq_90/cutadapt/K562_RNA-seq_90_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_RNA-seq_90/cutadapt/K562_RNA-seq_90_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` 0.2307 PEPPRO _RES_ ### Prealignments (06-15 07:30:56) elapsed: 0.0 _TIME_ Prealignment assemblies: ['human_rDNA'] ### Map to human_rDNA (06-15 07:30:56) 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 K562_RNA-seq_90 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/fastq/K562_RNA-seq_90_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/prealignments/K562_RNA-seq_90_human_rDNA_unmap.fq 2>&1 > /dev/null)` Missing stat 'Aligned_reads_human_rDNA' 69824899 reads; of these: 69824899 (100.00%) were unpaired; of these: 67733278 (97.00%) aligned 0 times 2091621 (3.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 3.00% overall alignment rate > `Aligned_reads_human_rDNA` 2091621.0 PEPPRO _RES_ > `Alignment_rate_human_rDNA` 3.0 PEPPRO _RES_ ### Map to genome (06-15 07:38:17) elapsed: 441.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam` > `bowtie2 -p 12 --very-sensitive --rg-id K562_RNA-seq_90 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/prealignments/K562_RNA-seq_90_human_rDNA_unmap.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/tmpec71bnbl -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_temp.bam` (343849,343855,343856)
67733278 reads; of these:
  67733278 (100.00%) were unpaired; of these:
    10447568 (15.42%) aligned 0 times
    34858767 (51.46%) aligned exactly 1 time
    22426943 (33.11%) aligned >1 times
84.58% overall alignment rate
[bam_sort_core] merging from 22 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:37:42. Running peak memory: 4.107GB. PID: 343849; Command: bowtie2; Return code: 0; Memory used: 3.709GB PID: 343855; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 343856; Command: samtools; Return code: 0; Memory used: 0.89GB > `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam` (347581)

Command completed. Elapsed time: 0:03:33. Running peak memory: 4.107GB.  
  PID: 347581;	Command: samtools;	Return code: 0;	Memory used: 0.019GB


> `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_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`

> `Mapped_reads`	57285710	PEPPRO	_RES_

> `QC_filtered_reads`	12079693	PEPPRO	_RES_

> `Aligned_reads`	45206017	PEPPRO	_RES_

> `Alignment_rate`	64.74	PEPPRO	_RES_

> `Total_efficiency`	64.58	PEPPRO	_RES_

> `Read_depth`	9.03	PEPPRO	_RES_

### Compress all unmapped read files (06-15 08:34:54) elapsed: 3397.0 _TIME_

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/prealignments/K562_RNA-seq_90_human_rDNA_unmap.fq.gz`  

> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/prealignments/K562_RNA-seq_90_human_rDNA_unmap.fq` (349233)

Command completed. Elapsed time: 0:02:27. Running peak memory: 4.107GB.  
  PID: 349233;	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/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_temp.bam.bai`  

> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_temp.bam` (349606)

Command completed. Elapsed time: 0:01:09. Running peak memory: 4.107GB.  
  PID: 349606;	Command: samtools;	Return code: 0;	Memory used: 0.016GB


> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`

> `Mitochondrial_reads`	3902862	PEPPRO	_RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_noMT.bam`  

> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam` (349669)

Command completed. Elapsed time: 0:00:46. Running peak memory: 4.107GB.  
  PID: 349669;	Command: samtools;	Return code: 0;	Memory used: 0.016GB


> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam | cut -f 1-2 | awk '{print $1, 0, $2}' | grep -vwe 'chrM' -vwe 'chrMT' -vwe 'M' -vwe 'MT' -vwe 'rCRSd' -vwe 'rCRSd_3k' > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/chr_sizes.bed` (349708,349709,349710,349711)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 349708;	Command: samtools;	Return code: 0;	Memory used: 0.0GB  
  PID: 349710;	Command: awk;	Return code: 0;	Memory used: 0.0GB  
  PID: 349709;	Command: cut;	Return code: 0;	Memory used: 0.0GB  
  PID: 349711;	Command: grep;	Return code: 0;	Memory used: 0.0GB


> `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_noMT.bam` (349713)

Command completed. Elapsed time: 0:00:53. Running peak memory: 4.107GB.  
  PID: 349713;	Command: samtools;	Return code: 0;	Memory used: 0.02GB


> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam` (350010)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 350010;	Command: mv;	Return code: 0;	Memory used: 0.002GB


> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam` (350012)

Command completed. Elapsed time: 0:00:43. Running peak memory: 4.107GB.  
  PID: 350012;	Command: samtools;	Return code: 0;	Memory used: 0.008GB

Missing stat 'Maximum_read_length'

> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_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 08:43:05) elapsed: 491.0 _TIME_

Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam.bai`  
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_bamQC.tsv`  

> `/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_bamQC.tsv` (350168)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/tmp_K562_RNA-seq_90_sort_ir3x_bwx'
Processing with 12 cores...
Discarding 101 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr22_KI270737v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', '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_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1']
Keeping 94 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_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_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270583v1', 'chrUn_KI270580v1', 'chrUn_KI270589v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270330v1', '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: 0:00:48. Running peak memory: 4.107GB. PID: 350168; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 2.507GB > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_bamQC.tsv` > `NRF` 0.54 PEPPRO _RES_ > `PBC1` 0.83 PEPPRO _RES_ > `PBC2` 11.16 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_unmap.bam` > `samtools view -b -@ 12 -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_unmap.bam` (350236)

Command completed. Elapsed time: 0:00:23. Running peak memory: 4.107GB.  
  PID: 350236;	Command: samtools;	Return code: 0;	Memory used: 0.018GB


> `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_temp.bam`

> `Unmapped_reads`	10447568	PEPPRO	_RES_

### Split BAM by strand (06-15 08:44:27) elapsed: 82.0 _TIME_

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam`  

> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam` (350295)

Command completed. Elapsed time: 0:03:24. Running peak memory: 4.107GB.  
  PID: 350295;	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_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam` (350663)

Command completed. Elapsed time: 0:03:17. Running peak memory: 4.107GB.  
  PID: 350663;	Command: samtools;	Return code: 0;	Memory used: 0.006GB


### Calculate TSS enrichment (06-15 08:51:09) elapsed: 401.0 _TIME_

Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/minus_TSS.tsv`  

> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (351066)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351066;	Command: sed;	Return code: 0;	Memory used: 0.002GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_plus_TssEnrichment.txt`  

> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_plus_TssEnrichment.txt` (351067)

Command completed. Elapsed time: 0:00:10. Running peak memory: 4.107GB.  
  PID: 351067;	Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py;	Return code: 0;	Memory used: 0.517GB


> `TSS_coding_score`	18.6	PEPPRO	_RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_minus_TssEnrichment.txt`  

> `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_minus_TssEnrichment.txt` (351103)

Command completed. Elapsed time: 0:00:07. Running peak memory: 4.107GB.  
  PID: 351103;	Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py;	Return code: 0;	Memory used: 0.616GB


> `TSS_non-coding_score`	3.0	PEPPRO	_RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_TSSenrichment.pdf`  

> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_minus_TssEnrichment.txt` (351136)

Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_minus_TssEnrichment.txt
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
TSS enrichment plot completed!

Command completed. Elapsed time: 0:00:06. Running peak memory: 4.107GB. PID: 351136; Command: Rscript; Return code: 0; Memory used: 0.316GB > `TSS enrichment` QC_hg38/K562_RNA-seq_90_TSSenrichment.pdf TSS enrichment QC_hg38/K562_RNA-seq_90_TSSenrichment.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt` > `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_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_RNA-seq_90/QC_hg38/chr_order.txt` (351160,351161,351162,351163)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351160;	Command: samtools;	Return code: 0;	Memory used: 0.0GB  
  PID: 351162;	Command: awk;	Return code: 0;	Memory used: 0.0GB  
  PID: 351161;	Command: grep;	Return code: 0;	Memory used: 0.0GB  
  PID: 351163;	Command: awk;	Return code: 0;	Memory used: 0.0GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_keep.txt`  

> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_keep.txt` (351165)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351165;	Command: cut;	Return code: 0;	Memory used: 0.0GB


### Calculate Pause Index (PI) (06-15 08:51:33) elapsed: 24.0 _TIME_

Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_ensembl_gene_body.bed`  

> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_TSS.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_ensembl_tss.bed` (351167,351168)

Command completed. Elapsed time: 0:00:02. Running peak memory: 4.107GB.  
  PID: 351167;	Command: grep;	Return code: 0;	Memory used: 0.004GB  
  PID: 351168;	Command: bedtools;	Return code: 0;	Memory used: 0.093GB


> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_gene_body.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_ensembl_gene_body.bed` (351172,351173)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351172;	Command: grep;	Return code: 0;	Memory used: 0.003GB  
  PID: 351173;	Command: bedtools;	Return code: 0;	Memory used: 0.005GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_TSS_density.bed`  

> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4,4 -k7,7nr | sort -k4,4 -u > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_TSS_density.bed` (351175,351176,351177,351178)

Command completed. Elapsed time: 0:01:10. Running peak memory: 4.107GB.  
  PID: 351176;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 351178;	Command: sort;	Return code: 0;	Memory used: 0.002GB  
  PID: 351175;	Command: bedtools;	Return code: 0;	Memory used: 0.066GB  
  PID: 351177;	Command: sort;	Return code: 0;	Memory used: 0.005GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_gene_body_density.bed`  

> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_gene_body_density.bed` (351238,351239,351240)

Command completed. Elapsed time: 0:01:43. Running peak memory: 4.107GB.  
  PID: 351238;	Command: bedtools;	Return code: 0;	Memory used: 0.29GB  
  PID: 351240;	Command: sort;	Return code: 0;	Memory used: 0.005GB  
  PID: 351239;	Command: awk;	Return code: 0;	Memory used: 0.001GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_pause_index.bed`  

> `join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_gene_body_density.bed | awk -v OFS='	' '{ if ($5 == "+"){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2), ($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}' | env LC_COLLATE=C sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/tmp1htwvuce` (351325,351326,351327)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351325;	Command: join;	Return code: 0;	Memory used: 0.001GB  
  PID: 351327;	Command: env;	Return code: 0;	Memory used: 0.004GB  
  PID: 351326;	Command: awk;	Return code: 0;	Memory used: 0.001GB


> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/tmp1htwvuce | 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_RNA-seq_90/QC_hg38/K562_RNA-seq_90_pause_index.bed`  

> `awk -v OFS='	' '{ if ($5 > 0.0394495) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/tmp1htwvuce > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_pause_index.bed` (351333)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351333;	Command: awk;	Return code: 0;	Memory used: 0.002GB


> `sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_pause_index.bed | awk ' { a[i++]=$5; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'`

> `Pause_index`	7.62	PEPPRO	_RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_pause_index.pdf`  

> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R pi --annotate -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_pause_index.bed` (351338)
Pause index plot completed!

Command completed. Elapsed time: 0:00:05. Running peak memory: 4.107GB. PID: 351338; Command: Rscript; Return code: 0; Memory used: 0.285GB > `Pause index` QC_hg38/K562_RNA-seq_90_pause_index.pdf Pause index QC_hg38/K562_RNA-seq_90_pause_index.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_pause_index.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_pause_index.bed` (351359)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351359;	Command: pigz;	Return code: 0;	Memory used: 0.002GB


### Calculate Fraction of Reads in pre-mature mRNA (06-15 08:54:34) elapsed: 181.0 _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_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam`
45206017 17848511

> `Plus_FRiP`	0.39	PEPPRO	_RES_
Missing stat 'Minus_FRiP'

> `samtools view -@ 4 -c -L /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam`
45206017 18041807

> `Minus_FRiP`	0.4	PEPPRO	_RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_gene_coverage.bed`  

> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_gene_sort.bed` (351640,351642)

Command completed. Elapsed time: 0:00:02. Running peak memory: 4.107GB.  
  PID: 351640;	Command: grep;	Return code: 0;	Memory used: 0.004GB  
  PID: 351642;	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_RNA-seq_90/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_gene_coverage.bed` (351644)

Command completed. Elapsed time: 0:01:46. Running peak memory: 4.107GB.  
  PID: 351644;	Command: bedtools;	Return code: 0;	Memory used: 0.249GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/hg38_annotations.bed`  

> `ln -sf /project/shefflab/genomes/hg38/feat_annotation/default/hg38_annotations.bed.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/hg38_annotations.bed.gz` (351733)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351733;	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/K562_RNA-seq_90/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/hg38_annotations.bed` (351734)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351734;	Command: pigz;	Return code: 0;	Memory used: 0.002GB


### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 08:57:38) elapsed: 184.0 _TIME_


> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Enhancer`  

> `awk -F'	' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/raw/hg38_annotations.bed` (351743)

Command completed. Elapsed time: 0:00:01. Running peak memory: 4.107GB.  
  PID: 351743;	Command: awk;	Return code: 0;	Memory used: 0.002GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Enhancer_sort.bed`  

> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Enhancer_sort.bed` (351746,351747,351748,351749)

Command completed. Elapsed time: 0:00:01. Running peak memory: 4.107GB.  
  PID: 351746;	Command: cut;	Return code: 0;	Memory used: 0.0GB  
  PID: 351747;	Command: grep;	Return code: 0;	Memory used: 0.002GB  
  PID: 351749;	Command: bedtools;	Return code: 0;	Memory used: 0.044GB  
  PID: 351748;	Command: cut;	Return code: 0;	Memory used: 0.001GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Enhancer_plus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Enhancer_plus_coverage.bed` (351752)

Command completed. Elapsed time: 0:00:33. Running peak memory: 4.107GB.  
  PID: 351752;	Command: bedtools;	Return code: 0;	Memory used: 0.035GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Enhancer_minus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Enhancer_minus_coverage.bed` (351780)

Command completed. Elapsed time: 0:00:31. Running peak memory: 4.107GB.  
  PID: 351780;	Command: bedtools;	Return code: 0;	Memory used: 0.045GB

Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter`  
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_sort.bed`  

> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_sort.bed` (351807,351808,351809,351810)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351807;	Command: cut;	Return code: 0;	Memory used: 0.0GB  
  PID: 351808;	Command: grep;	Return code: 0;	Memory used: 0.003GB  
  PID: 351810;	Command: bedtools;	Return code: 0;	Memory used: 0.009GB  
  PID: 351809;	Command: cut;	Return code: 0;	Memory used: 0.001GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_plus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_plus_coverage.bed` (351812)

Command completed. Elapsed time: 0:00:38. Running peak memory: 4.107GB.  
  PID: 351812;	Command: bedtools;	Return code: 0;	Memory used: 0.176GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_minus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_minus_coverage.bed` (351845)

Command completed. Elapsed time: 0:00:34. Running peak memory: 4.107GB.  
  PID: 351845;	Command: bedtools;	Return code: 0;	Memory used: 0.084GB

Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter Flanking Region`  
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_Flanking_Region`  

> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_Flanking_Region"` (351875)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 351875;	Command: mv;	Return code: 0;	Memory used: 0.002GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed`  

> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed` (351876,351877,351878,351879)

Command completed. Elapsed time: 0:00:01. Running peak memory: 4.107GB.  
  PID: 351876;	Command: cut;	Return code: 0;	Memory used: 0.0GB  
  PID: 351878;	Command: cut;	Return code: 0;	Memory used: 0.001GB  
  PID: 351877;	Command: grep;	Return code: 0;	Memory used: 0.002GB  
  PID: 351879;	Command: bedtools;	Return code: 0;	Memory used: 0.01GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_Flanking_Region_plus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_Flanking_Region_plus_coverage.bed` (351882)

Command completed. Elapsed time: 0:00:34. Running peak memory: 4.107GB.  
  PID: 351882;	Command: bedtools;	Return code: 0;	Memory used: 0.025GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_Flanking_Region_minus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_Flanking_Region_minus_coverage.bed` (352169)

Command completed. Elapsed time: 0:00:33. Running peak memory: 4.107GB.  
  PID: 352169;	Command: bedtools;	Return code: 0;	Memory used: 0.063GB

Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/5' UTR`  
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/5_UTR`  

> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/5_UTR"` (352210)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 352210;	Command: mv;	Return code: 0;	Memory used: 0.002GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/5_UTR_sort.bed`  

> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/5_UTR_sort.bed` (352211,352212,352213,352214)

Command completed. Elapsed time: 0:00:01. Running peak memory: 4.107GB.  
  PID: 352211;	Command: cut;	Return code: 0;	Memory used: 0.0GB  
  PID: 352212;	Command: grep;	Return code: 0;	Memory used: 0.003GB  
  PID: 352214;	Command: bedtools;	Return code: 0;	Memory used: 0.03GB  
  PID: 352213;	Command: cut;	Return code: 0;	Memory used: 0.001GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_5_UTR_plus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_5_UTR_plus_coverage.bed` (352217)

Command completed. Elapsed time: 0:00:34. Running peak memory: 4.107GB.  
  PID: 352217;	Command: bedtools;	Return code: 0;	Memory used: 0.029GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_5_UTR_minus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_5_UTR_minus_coverage.bed` (352247)

Command completed. Elapsed time: 0:00:33. Running peak memory: 4.107GB.  
  PID: 352247;	Command: bedtools;	Return code: 0;	Memory used: 0.036GB

Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/3' UTR`  
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/3_UTR`  

> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/3_UTR"` (352275)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 352275;	Command: mv;	Return code: 0;	Memory used: 0.002GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/3_UTR_sort.bed`  

> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/3_UTR_sort.bed` (352276,352277,352278,352279)

Command completed. Elapsed time: 0:00:01. Running peak memory: 4.107GB.  
  PID: 352276;	Command: cut;	Return code: 0;	Memory used: 0.0GB  
  PID: 352277;	Command: grep;	Return code: 0;	Memory used: 0.003GB  
  PID: 352279;	Command: bedtools;	Return code: 0;	Memory used: 0.034GB  
  PID: 352278;	Command: cut;	Return code: 0;	Memory used: 0.001GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_3_UTR_plus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_3_UTR_plus_coverage.bed` (352282)

Command completed. Elapsed time: 0:00:37. Running peak memory: 4.107GB.  
  PID: 352282;	Command: bedtools;	Return code: 0;	Memory used: 0.055GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_3_UTR_minus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_3_UTR_minus_coverage.bed` (352315)

Command completed. Elapsed time: 0:00:39. Running peak memory: 4.107GB.  
  PID: 352315;	Command: bedtools;	Return code: 0;	Memory used: 0.069GB

Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Exon`  
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Exon_sort.bed`  

> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Exon_sort.bed` (352348,352349,352350,352351)

Command completed. Elapsed time: 0:00:03. Running peak memory: 4.107GB.  
  PID: 352348;	Command: cut;	Return code: 0;	Memory used: 0.0GB  
  PID: 352349;	Command: grep;	Return code: 0;	Memory used: 0.004GB  
  PID: 352351;	Command: bedtools;	Return code: 0;	Memory used: 0.158GB  
  PID: 352350;	Command: cut;	Return code: 0;	Memory used: 0.001GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Exon_plus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Exon_plus_coverage.bed` (352355)

Command completed. Elapsed time: 0:00:48. Running peak memory: 4.107GB.  
  PID: 352355;	Command: bedtools;	Return code: 0;	Memory used: 0.224GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Exon_minus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Exon_minus_coverage.bed` (352397)

Command completed. Elapsed time: 0:00:45. Running peak memory: 4.107GB.  
  PID: 352397;	Command: bedtools;	Return code: 0;	Memory used: 0.12GB

Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Intron`  
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Intron_sort.bed`  

> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Intron_sort.bed` (352627,352628,352629,352630)

Command completed. Elapsed time: 0:00:01. Running peak memory: 4.107GB.  
  PID: 352627;	Command: cut;	Return code: 0;	Memory used: 0.0GB  
  PID: 352629;	Command: cut;	Return code: 0;	Memory used: 0.001GB  
  PID: 352628;	Command: grep;	Return code: 0;	Memory used: 0.002GB  
  PID: 352630;	Command: bedtools;	Return code: 0;	Memory used: 0.077GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Intron_plus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Intron_plus_coverage.bed` (352633)

Command completed. Elapsed time: 0:00:40. Running peak memory: 4.107GB.  
  PID: 352633;	Command: bedtools;	Return code: 0;	Memory used: 0.164GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Intron_minus_coverage.bed`  

> `bedtools coverage -sorted  -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Intron_minus_coverage.bed` (352669)

Command completed. Elapsed time: 0:00:39. Running peak memory: 4.107GB.  
  PID: 352669;	Command: bedtools;	Return code: 0;	Memory used: 0.081GB


### Plot cFRiF/FRiF (06-15 09:06:27) elapsed: 529.0 _TIME_


> `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_cFRiF.pdf`  

> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_RNA-seq_90 -z 3099922541 -n 20980700 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Intron_plus_coverage.bed` (352721)
Cumulative cfrif plot completed!

Command completed. Elapsed time: 0:00:39. Running peak memory: 4.107GB. PID: 352721; Command: Rscript; Return code: 0; Memory used: 0.44GB > `cFRiF` QC_hg38/K562_RNA-seq_90_cFRiF.pdf cFRiF QC_hg38/K562_RNA-seq_90_cFRiF.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_FRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_RNA-seq_90 -z 3099922541 -n 20980700 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_Intron_plus_coverage.bed` (352796)
Cumulative frif plot completed!

Command completed. Elapsed time: 0:00:29. Running peak memory: 4.107GB. PID: 352796; Command: Rscript; Return code: 0; Memory used: 0.437GB > `FRiF` QC_hg38/K562_RNA-seq_90_FRiF.pdf FRiF QC_hg38/K562_RNA-seq_90_FRiF.png PEPPRO _OBJ_ ### Calculate mRNA contamination (06-15 09:07:38) elapsed: 71.0 _TIME_ Missing stat 'mRNA_contamination' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_introns_sort.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_exons.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_exons_sort.bed` (352831,352832)

Command completed. Elapsed time: 0:00:05. Running peak memory: 4.107GB.  
  PID: 352832;	Command: bedtools;	Return code: 0;	Memory used: 0.086GB  
  PID: 352831;	Command: grep;	Return code: 0;	Memory used: 0.004GB


> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_introns.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_introns_sort.bed` (352839,352840,352841)

Command completed. Elapsed time: 0:00:05. Running peak memory: 4.107GB.  
  PID: 352839;	Command: grep;	Return code: 0;	Memory used: 0.005GB  
  PID: 352841;	Command: bedtools;	Return code: 0;	Memory used: 0.004GB  
  PID: 352840;	Command: bedtools;	Return code: 0;	Memory used: 0.033GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_introns_coverage.bed`  

> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exons_coverage.bed` (352848)

Command completed. Elapsed time: 0:01:25. Running peak memory: 4.107GB.  
  PID: 352848;	Command: bedtools;	Return code: 0;	Memory used: 0.2GB


> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_introns_coverage.bed` (352918)

Command completed. Elapsed time: 0:01:21. Running peak memory: 4.107GB.  
  PID: 352918;	Command: bedtools;	Return code: 0;	Memory used: 0.19GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exons_rpkm.bed`  

> `awk -v OFS='	' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/45.206017)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exons_rpkm.bed` (353236,353237,353238)

Command completed. Elapsed time: 0:00:01. Running peak memory: 4.107GB.  
  PID: 353236;	Command: awk;	Return code: 0;	Memory used: 0.007GB  
  PID: 353238;	Command: sort;	Return code: 0;	Memory used: 0.004GB  
  PID: 353237;	Command: awk;	Return code: 0;	Memory used: 0.001GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_introns_rpkm.bed`  

> `awk -v OFS='	' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/45.206017)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_introns_rpkm.bed` (353241,353242,353243)

Command completed. Elapsed time: 0:00:01. Running peak memory: 4.107GB.  
  PID: 353241;	Command: awk;	Return code: 0;	Memory used: 0.008GB  
  PID: 353243;	Command: sort;	Return code: 0;	Memory used: 0.003GB  
  PID: 353242;	Command: awk;	Return code: 0;	Memory used: 0.001GB

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exon_intron_ratios.bed`  

> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exons_rpkm.bed | awk -v OFS='	' 'NF==11 {print $7, $8, $9, $1, ($10/$5), $11}' | sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exon_intron_ratios.bed` (353245,353246,353247)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 353245;	Command: join;	Return code: 0;	Memory used: 0.001GB  
  PID: 353247;	Command: sort;	Return code: 0;	Memory used: 0.004GB  
  PID: 353246;	Command: awk;	Return code: 0;	Memory used: 0.001GB


> `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exon_intron_ratios.bed | sort -n | awk ' { a[i++]=$1; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'`

> `mRNA_contamination`	9.16	PEPPRO	_RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_mRNA_contamination.pdf`  

> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exon_intron_ratios.bed --annotate` (353253)
mRNA contamination plot completed!

Command completed. Elapsed time: 0:00:05. Running peak memory: 4.107GB. PID: 353253; Command: Rscript; Return code: 0; Memory used: 0.278GB > `mRNA contamination` QC_hg38/K562_RNA-seq_90_mRNA_contamination.pdf mRNA contamination QC_hg38/K562_RNA-seq_90_mRNA_contamination.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exon_intron_ratios.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/QC_hg38/K562_RNA-seq_90_exon_intron_ratios.bed` (353275)

Command completed. Elapsed time: 0:00:00. Running peak memory: 4.107GB.  
  PID: 353275;	Command: pigz;	Return code: 0;	Memory used: 0.003GB


### Produce bigWig files (06-15 09:10:41) elapsed: 183.0 _TIME_

Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_plus_smooth_body_0-mer.bw`  

> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam` (353283)

Command completed. Elapsed time: 0:00:21. Running peak memory: 4.107GB.  
  PID: 353283;	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/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 45206017.0` (353301)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_plus.bam'
Temporary files will be stored in: 'tmp_K562_RNA-seq_90_plus_cuttrace_0uayre8d'
Processing with 4 cores...
Discarding 111 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr15_KI270727v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_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_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_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', '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_GL000226v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1']
Keeping 84 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_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_KI270726v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270580v1', 'chrUn_KI270589v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270330v1', '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 84 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_plus_exact_body_0-mer.bw'
Merging 84 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:08:12. Running peak memory: 4.107GB. PID: 353301; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.585GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_minus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam` (354707)

Command completed. Elapsed time: 0:00:21. Running peak memory: 4.107GB.  
  PID: 354707;	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/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 45206017.0` (354725)
Cutting parallel chroms in half to accommodate two tracks.
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/aligned_hg38/K562_RNA-seq_90_minus.bam'
Temporary files will be stored in: 'tmp_K562_RNA-seq_90_minus_cuttrace_6zkg5ahi'
Processing with 4 cores...
Discarding 117 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr14_KI270723v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270735v1_random', 'chr22_KI270737v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', '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_KI270521v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1', '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_KI270708v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_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_KI270725v1_random', 'chr14_KI270726v1_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', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270583v1', 'chrUn_KI270589v1', 'chrUn_KI270330v1', 'chrUn_KI270448v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1']
Reduce step (merge files)...
Merging 78 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_minus_exact_body_0-mer.bw'
Merging 78 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_90/signal_hg38/K562_RNA-seq_90_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:07:02. Running peak memory: 4.107GB. PID: 354725; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.704GB ### Pipeline completed. Epilogue * Elapsed time (this run): 2:09:26 * Total elapsed time (all runs): 2:45:17 * Peak memory (this run): 4.1066 GB * Pipeline completed time: 2020-06-15 09:26:37