PEPPRO log - peppro

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

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