### Pipeline run code and environment:
* Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name K562_RNA-seq_100 --genome hg38 --input /project/shefflab/data//guertin/fastq/K562_100pctRNA.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-ba26-33c0
* Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
* Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/
* 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_100pctRNA.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_100`
* `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_100pctRNA.fastq.gz
> `File_mb` 5091.82 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_100/raw/K562_RNA-seq_100.fastq.gz`
> `ln -sf /project/shefflab/data//guertin/fastq/K562_100pctRNA.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/raw/K562_RNA-seq_100.fastq.gz` (52656)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB.
PID: 52656; 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_100/raw/K562_RNA-seq_100.fastq.gz'
Found .fastq.gz file
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_R1.fastq`
> `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/raw/K562_RNA-seq_100.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_R1.fastq` (52657)
Command completed. Elapsed time: 0:02:35. Running peak memory: 0.002GB.
PID: 52657; 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_100/raw/K562_RNA-seq_100.fastq.gz']
### FASTQ processing: (06-15 07:21:10) elapsed: 237.0 _TIME_
> `cutadapt --version`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_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_100/fastq/K562_RNA-seq_100_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/cutadapt/K562_RNA-seq_100_R1_cutadapt.txt` (53122)
Command completed. Elapsed time: 0:01:53. Running peak memory: 5.727GB.
PID: 53122; Command: cutadapt; Return code: 0; Memory used: 5.727GB
> `seqtk trimfq -b 0 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_R1_noadap.fastq | seqtk seq -L 2 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_R1_processed.fastq` (53248,53249)
Command completed. Elapsed time: 0:01:58. Running peak memory: 5.727GB.
PID: 53248; Command: seqtk; Return code: 0; Memory used: 0.001GB
PID: 53249; 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_100/cutadapt/K562_RNA-seq_100_R1_cutadapt.txt | awk '{print $(NF-1)}'`
> `Reads_with_adapter` 24858626.0 PEPPRO _RES_
> `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/cutadapt/K562_RNA-seq_100_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_100/cutadapt/K562_RNA-seq_100_R1_cutadapt.txt`
> `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_R1_short.fastq | awk '{print $1}'`
> `Uninformative_adapter_reads` 0.0 PEPPRO _RES_
> `Pct_uninformative_adapter_reads` 0.0 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastqc/K562_RNA-seq_100_R1_processed_fastqc.html`
> `echo '### Calculate the number of trimmed reads'` (53615)
### Calculate the number of trimmed reads
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 53615; Command: echo; Return code: 0; Memory used: 0.0GB
Evaluating read trimming
> `Trimmed_reads` 70000000 PEPPRO _RES_
> `Trim_loss_rate` 0.0 PEPPRO _RES_
Targetless command, running...
> `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_R1_processed.fastq` (53636)
Started analysis of K562_RNA-seq_100_R1_processed.fastq
Approx 5% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 10% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 15% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 20% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 25% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 30% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 35% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 40% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 45% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 50% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 55% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 60% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 65% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 70% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 75% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 80% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 85% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 90% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 95% complete for K562_RNA-seq_100_R1_processed.fastq
Approx 100% complete for K562_RNA-seq_100_R1_processed.fastq
Analysis complete for K562_RNA-seq_100_R1_processed.fastq
Command completed. Elapsed time: 0:04:35. Running peak memory: 5.727GB.
PID: 53636; Command: fastqc; Return code: 0; Memory used: 0.201GB
> `FastQC report r1` fastqc/K562_RNA-seq_100_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_100/fastq/processed_R1.flag`
> `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/processed_R1.flag` (54166)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 54166; Command: touch; Return code: 0; Memory used: 0.002GB
### Plot adapter insertion distribution (06-15 07:30:55) elapsed: 585.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/cutadapt/K562_RNA-seq_100_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_100/cutadapt/K562_RNA-seq_100_R1_cutadapt.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/cutadapt` (54167)
Adapter insertion distribution plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.727GB.
PID: 54167; Command: Rscript; Return code: 0; Memory used: 0.3GB
> `Adapter insertion distribution` cutadapt/K562_RNA-seq_100_R1_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/K562_RNA-seq_100_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_100/cutadapt/K562_RNA-seq_100_R1_cutadapt.txt | awk 'NR>2 {print prev} {prev=$0}' | awk '{if ($3/$2 < 0.01) print $1, $2}' | awk 'BEGIN{max= 0; max_len=0; len=0}{if ($2>0+max) {max=$2; len=$1}; max_len=$1} END{print max_len-len}'`
> `Peak_adapter_insertion_size` 0 PEPPRO _RES_
Missing stat 'Degradation_ratio'
### Calculating degradation ratio (06-15 07:31:00) elapsed: 5.0 _TIME_
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/cutadapt/K562_RNA-seq_100_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_100/cutadapt/K562_RNA-seq_100_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_100/cutadapt/K562_RNA-seq_100_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_100/cutadapt/K562_RNA-seq_100_R1_cutadapt.txt | awk '{ if ($1 == 40) {status = 1}} END {if (status) {print status} else {print 0}}'`
> `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/cutadapt/K562_RNA-seq_100_R1_cutadapt.txt | awk 'END {print $1}'`
> `awk '/count/,0' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/cutadapt/K562_RNA-seq_100_R1_cutadapt.txt | awk 'NR>2 {print prev} {prev=$0}' | awk '{if ($3/$2 < 0.01) print $1, $2}' | awk '{a[NR]=$1; b[NR]=$2; max_len=$1}{if ($1 > max_len) {max_len=$1}} END{ for (i in a) print 1+max_len-a[i], b[i]}' | sort -nk1 | awk '($1 <= 10 && $1 >= 16){degradedSum += $2}; ($1 >= 6 && $1 <= 0){intactSum += $2} END {if (intactSum < 1) {intactSum = 1} print degradedSum/intactSum}'`
> `Degradation_ratio` 0.0 PEPPRO _RES_
### Prealignments (06-15 07:31:00) elapsed: 0.0 _TIME_
Prealignment assemblies: ['human_rDNA']
### Map to human_rDNA (06-15 07:31:00) 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_100 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/fastq/K562_RNA-seq_100_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/prealignments/K562_RNA-seq_100_human_rDNA_unmap.fq 2>&1 > /dev/null)`
Missing stat 'Aligned_reads_human_rDNA'
70000000 reads; of these:
70000000 (100.00%) were unpaired; of these:
68375974 (97.68%) aligned 0 times
1624026 (2.32%) aligned exactly 1 time
0 (0.00%) aligned >1 times
2.32% overall alignment rate
> `Aligned_reads_human_rDNA` 1624026.0 PEPPRO _RES_
> `Alignment_rate_human_rDNA` 2.32 PEPPRO _RES_
### Map to genome (06-15 07:39:19) elapsed: 500.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam`
> `bowtie2 -p 12 --very-sensitive --rg-id K562_RNA-seq_100 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/prealignments/K562_RNA-seq_100_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_100/aligned_hg38/tmpd6hrvyrl -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_temp.bam` (54845,54852,54853)
68375974 reads; of these:
68375974 (100.00%) were unpaired; of these:
11525030 (16.86%) aligned 0 times
33591968 (49.13%) aligned exactly 1 time
23258976 (34.02%) aligned >1 times
83.14% overall alignment rate
[bam_sort_core] merging from 22 files and 1 in-memory blocks...
Command completed. Elapsed time: 0:36:44. Running peak memory: 5.727GB.
PID: 54845; Command: bowtie2; Return code: 0; Memory used: 3.692GB
PID: 54852; Command: samtools; Return code: 0; Memory used: 0.004GB
PID: 54853; 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_100/aligned_hg38/K562_RNA-seq_100_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam` (58535)
Command completed. Elapsed time: 0:03:54. Running peak memory: 5.727GB.
PID: 58535; 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_100/aligned_hg38/K562_RNA-seq_100_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'`
> `Mapped_reads` 56850944 PEPPRO _RES_
> `QC_filtered_reads` 12689564 PEPPRO _RES_
> `Aligned_reads` 44161380 PEPPRO _RES_
> `Alignment_rate` 63.09 PEPPRO _RES_
> `Total_efficiency` 63.09 PEPPRO _RES_
> `Read_depth` 11.83 PEPPRO _RES_
### Compress all unmapped read files (06-15 08:32:47) elapsed: 3208.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/prealignments/K562_RNA-seq_100_human_rDNA_unmap.fq.gz`
> `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/prealignments/K562_RNA-seq_100_human_rDNA_unmap.fq` (60113)
Command completed. Elapsed time: 0:02:33. Running peak memory: 5.727GB.
PID: 60113; 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_100/aligned_hg38/K562_RNA-seq_100_temp.bam.bai`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_temp.bam` (60471)
Command completed. Elapsed time: 0:01:14. Running peak memory: 5.727GB.
PID: 60471; Command: samtools; Return code: 0; Memory used: 0.015GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3`
> `Mitochondrial_reads` 4192362 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_noMT.bam`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam` (60538)
Command completed. Elapsed time: 0:00:49. Running peak memory: 5.727GB.
PID: 60538; Command: samtools; Return code: 0; Memory used: 0.014GB
> `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_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_100/aligned_hg38/chr_sizes.bed` (60579,60580,60581,60582)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 60579; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 60581; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 60580; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 60582; 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_100/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_noMT.bam` (60584)
Command completed. Elapsed time: 0:00:53. Running peak memory: 5.727GB.
PID: 60584; Command: samtools; Return code: 0; Memory used: 0.02GB
> `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam` (60644)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 60644; Command: mv; Return code: 0; Memory used: 0.002GB
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam` (60645)
Command completed. Elapsed time: 0:00:46. Running peak memory: 5.727GB.
PID: 60645; Command: samtools; Return code: 0; Memory used: 0.014GB
Missing stat 'Maximum_read_length'
> `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-`
> `Maximum_read_length` 76 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 08:41:13) elapsed: 505.0 _TIME_
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam.bai`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_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_100/aligned_hg38/K562_RNA-seq_100_sort.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_bamQC.tsv` (61041)
Configured logger 'root' using pararead v0.6
Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam'
Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/tmp_K562_RNA-seq_100_sort_iqht1p80'
Processing with 12 cores...
Discarding 104 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr9_KI270717v1_random', 'chr14_KI270723v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_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_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', '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_GL000213v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1']
Keeping 91 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', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270515v1', '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_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: 5.727GB.
PID: 61041; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.987GB
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_bamQC.tsv`
> `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_bamQC.tsv`
> `NRF` 0.47 PEPPRO _RES_
> `PBC1` 0.79 PEPPRO _RES_
> `PBC2` 8.82 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_unmap.bam`
> `samtools view -b -@ 12 -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_unmap.bam` (61111)
Command completed. Elapsed time: 0:00:24. Running peak memory: 5.727GB.
PID: 61111; 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_100/aligned_hg38/K562_RNA-seq_100_temp.bam`
> `Unmapped_reads` 11525030 PEPPRO _RES_
### Split BAM by strand (06-15 08:42:36) elapsed: 83.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam`
> `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam` (61169)
Command completed. Elapsed time: 0:03:43. Running peak memory: 5.727GB.
PID: 61169; 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_100/aligned_hg38/K562_RNA-seq_100_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam` (61550)
Command completed. Elapsed time: 0:03:22. Running peak memory: 5.727GB.
PID: 61550; Command: samtools; Return code: 0; Memory used: 0.006GB
### Calculate TSS enrichment (06-15 08:49:41) elapsed: 424.0 _TIME_
Missing stat 'TSS_non-coding_score'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/minus_TSS.tsv`
> `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (61718)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 61718; 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_100/QC_hg38/K562_RNA-seq_100_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_100/aligned_hg38/K562_RNA-seq_100_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/K562_RNA-seq_100_plus_TssEnrichment.txt` (61719)
Command completed. Elapsed time: 0:00:10. Running peak memory: 5.727GB.
PID: 61719; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.515GB
> `TSS_coding_score` 19.1 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_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_100/aligned_hg38/K562_RNA-seq_100_sort.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/K562_RNA-seq_100_minus_TssEnrichment.txt` (61754)
Command completed. Elapsed time: 0:00:07. Running peak memory: 5.727GB.
PID: 61754; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.59GB
> `TSS_non-coding_score` 2.5 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_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_100/QC_hg38/K562_RNA-seq_100_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_minus_TssEnrichment.txt` (61787)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_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: 5.727GB.
PID: 61787; Command: Rscript; Return code: 0; Memory used: 0.308GB
> `TSS enrichment` QC_hg38/K562_RNA-seq_100_TSSenrichment.pdf TSS enrichment QC_hg38/K562_RNA-seq_100_TSSenrichment.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt`
> `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_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_100/QC_hg38/chr_order.txt` (62048,62049,62050,62051)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62048; Command: samtools; Return code: 0; Memory used: 0.0GB
PID: 62050; Command: awk; Return code: 0; Memory used: 0.0GB
PID: 62049; Command: grep; Return code: 0; Memory used: 0.0GB
PID: 62051; 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_100/QC_hg38/chr_keep.txt`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_keep.txt` (62054)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62054; Command: cut; Return code: 0; Memory used: 0.002GB
### Calculate Pause Index (PI) (06-15 08:50:05) elapsed: 24.0 _TIME_
Missing stat 'Pause_index'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_ensembl_gene_body.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_ensembl_tss.bed` (62056,62057)
Command completed. Elapsed time: 0:00:02. Running peak memory: 5.727GB.
PID: 62056; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 62057; Command: bedtools; Return code: 0; Memory used: 0.093GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_ensembl_gene_body.bed` (62060,62061)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62060; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 62061; 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_100/QC_hg38/K562_RNA-seq_100_TSS_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/K562_RNA-seq_100_TSS_density.bed` (62063,62064,62065,62066)
Command completed. Elapsed time: 0:01:08. Running peak memory: 5.727GB.
PID: 62063; Command: bedtools; Return code: 0; Memory used: 0.072GB
PID: 62065; Command: sort; Return code: 0; Memory used: 0.01GB
PID: 62064; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 62066; Command: sort; Return code: 0; Memory used: 0.003GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_gene_body_density.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_gene_body_density.bed` (62127,62128,62129)
Command completed. Elapsed time: 0:01:46. Running peak memory: 5.727GB.
PID: 62127; Command: bedtools; Return code: 0; Memory used: 0.313GB
PID: 62129; Command: sort; Return code: 0; Memory used: 0.005GB
PID: 62128; 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_100/QC_hg38/K562_RNA-seq_100_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_100/QC_hg38/K562_RNA-seq_100_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_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_100/QC_hg38/tmpv201glls` (62218,62219,62220)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62218; Command: join; Return code: 0; Memory used: 0.001GB
PID: 62220; Command: env; Return code: 0; Memory used: 0.004GB
PID: 62219; 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_100/QC_hg38/tmpv201glls | 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_100/QC_hg38/K562_RNA-seq_100_pause_index.bed`
> `awk -v OFS=' ' '{ if ($5 > 0.0486842) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/tmpv201glls > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_pause_index.bed` (62226)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62226; 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_100/QC_hg38/K562_RNA-seq_100_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` 7.79 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_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_100/QC_hg38/K562_RNA-seq_100_pause_index.bed` (62232)
Pause index plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.727GB.
PID: 62232; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `Pause index` QC_hg38/K562_RNA-seq_100_pause_index.pdf Pause index QC_hg38/K562_RNA-seq_100_pause_index.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_pause_index.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_pause_index.bed` (62253)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62253; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate Fraction of Reads in pre-mature mRNA (06-15 08:53:07) elapsed: 183.0 _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_100/aligned_hg38/K562_RNA-seq_100_plus.bam`
44161380 17667752
> `Plus_FRiP` 0.4 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_100/aligned_hg38/K562_RNA-seq_100_minus.bam`
44161380 17985866
> `Minus_FRiP` 0.41 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_gene_coverage.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_gene_sort.bed` (62331,62332)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.727GB.
PID: 62331; Command: grep; Return code: 0; Memory used: 0.004GB
PID: 62332; 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_100/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_gene_coverage.bed` (62335)
Command completed. Elapsed time: 0:01:41. Running peak memory: 5.727GB.
PID: 62335; Command: bedtools; Return code: 0; Memory used: 0.269GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/raw/hg38_annotations.bed.gz` (62629)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62629; 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_100/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/raw/hg38_annotations.bed` (62630)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62630; Command: pigz; Return code: 0; Memory used: 0.002GB
### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 08:56:05) elapsed: 177.0 _TIME_
> `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/raw/hg38_annotations.bed | sort -u`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Enhancer`
> `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/raw/hg38_annotations.bed` (62639)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.727GB.
PID: 62639; 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_100/QC_hg38/Enhancer_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Enhancer_sort.bed` (62641,62642,62643,62644)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.727GB.
PID: 62641; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 62642; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 62644; Command: bedtools; Return code: 0; Memory used: 0.011GB
PID: 62643; 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_100/QC_hg38/K562_RNA-seq_100_Enhancer_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Enhancer_plus_coverage.bed` (62647)
Command completed. Elapsed time: 0:00:34. Running peak memory: 5.727GB.
PID: 62647; Command: bedtools; Return code: 0; Memory used: 0.038GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Enhancer_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Enhancer_minus_coverage.bed` (62676)
Command completed. Elapsed time: 0:00:34. Running peak memory: 5.727GB.
PID: 62676; Command: bedtools; Return code: 0; Memory used: 0.049GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter_sort.bed` (62706,62707,62708,62709)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62706; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 62707; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 62709; Command: bedtools; Return code: 0; Memory used: 0.008GB
PID: 62708; 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_100/QC_hg38/K562_RNA-seq_100_Promoter_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_plus_coverage.bed` (62711)
Command completed. Elapsed time: 0:00:38. Running peak memory: 5.727GB.
PID: 62711; Command: bedtools; Return code: 0; Memory used: 0.195GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_minus_coverage.bed` (62743)
Command completed. Elapsed time: 0:00:36. Running peak memory: 5.727GB.
PID: 62743; Command: bedtools; Return code: 0; Memory used: 0.09GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter Flanking Region`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter_Flanking_Region`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter_Flanking_Region"` (62776)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62776; 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_100/QC_hg38/Promoter_Flanking_Region_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed` (62777,62778,62779,62780)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.727GB.
PID: 62777; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 62779; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 62778; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 62780; Command: bedtools; Return code: 0; Memory used: 0.009GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_Flanking_Region_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_Flanking_Region_plus_coverage.bed` (62783)
Command completed. Elapsed time: 0:00:35. Running peak memory: 5.727GB.
PID: 62783; Command: bedtools; Return code: 0; Memory used: 0.026GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_Flanking_Region_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_Flanking_Region_minus_coverage.bed` (62812)
Command completed. Elapsed time: 0:00:32. Running peak memory: 5.727GB.
PID: 62812; Command: bedtools; Return code: 0; Memory used: 0.069GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/5' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/5_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/5_UTR"` (62841)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 62841; 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_100/QC_hg38/5_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/5_UTR_sort.bed` (62842,62843,62844,62845)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.727GB.
PID: 62842; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 62843; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 62845; Command: bedtools; Return code: 0; Memory used: 0.01GB
PID: 62844; 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_100/QC_hg38/K562_RNA-seq_100_5_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_5_UTR_plus_coverage.bed` (62848)
Command completed. Elapsed time: 0:00:34. Running peak memory: 5.727GB.
PID: 62848; Command: bedtools; Return code: 0; Memory used: 0.031GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_5_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_5_UTR_minus_coverage.bed` (63134)
Command completed. Elapsed time: 0:00:32. Running peak memory: 5.727GB.
PID: 63134; Command: bedtools; Return code: 0; Memory used: 0.039GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/3' UTR`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/3_UTR`
> `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/3_UTR"` (63196)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 63196; 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_100/QC_hg38/3_UTR_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/3_UTR_sort.bed` (63197,63198,63199,63200)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.727GB.
PID: 63197; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 63198; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 63200; Command: bedtools; Return code: 0; Memory used: 0.009GB
PID: 63199; 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_100/QC_hg38/K562_RNA-seq_100_3_UTR_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_3_UTR_plus_coverage.bed` (63203)
Command completed. Elapsed time: 0:00:39. Running peak memory: 5.727GB.
PID: 63203; Command: bedtools; Return code: 0; Memory used: 0.06GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_3_UTR_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_3_UTR_minus_coverage.bed` (63250)
Command completed. Elapsed time: 0:00:37. Running peak memory: 5.727GB.
PID: 63250; Command: bedtools; Return code: 0; Memory used: 0.076GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Exon`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Exon_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Exon_sort.bed` (63284,63285,63286,63287)
Command completed. Elapsed time: 0:00:03. Running peak memory: 5.727GB.
PID: 63284; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 63285; Command: grep; Return code: 0; Memory used: 0.003GB
PID: 63287; Command: bedtools; Return code: 0; Memory used: 0.158GB
PID: 63286; 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_100/QC_hg38/K562_RNA-seq_100_Exon_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Exon_plus_coverage.bed` (63291)
Command completed. Elapsed time: 0:00:48. Running peak memory: 5.727GB.
PID: 63291; Command: bedtools; Return code: 0; Memory used: 0.248GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Exon_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Exon_minus_coverage.bed` (63332)
Command completed. Elapsed time: 0:00:46. Running peak memory: 5.727GB.
PID: 63332; Command: bedtools; Return code: 0; Memory used: 0.132GB
Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Intron`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Intron_sort.bed`
> `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Intron_sort.bed` (63372,63373,63374,63375)
Command completed. Elapsed time: 0:00:02. Running peak memory: 5.727GB.
PID: 63372; Command: cut; Return code: 0; Memory used: 0.0GB
PID: 63374; Command: cut; Return code: 0; Memory used: 0.001GB
PID: 63373; Command: grep; Return code: 0; Memory used: 0.002GB
PID: 63375; 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_100/QC_hg38/K562_RNA-seq_100_Intron_plus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Intron_plus_coverage.bed` (63378)
Command completed. Elapsed time: 0:00:43. Running peak memory: 5.727GB.
PID: 63378; Command: bedtools; Return code: 0; Memory used: 0.18GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Intron_minus_coverage.bed`
> `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Intron_minus_coverage.bed` (63414)
Command completed. Elapsed time: 0:00:37. Running peak memory: 5.727GB.
PID: 63414; Command: bedtools; Return code: 0; Memory used: 0.089GB
### Plot cFRiF/FRiF (06-15 09:05:01) elapsed: 536.0 _TIME_
> `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam`
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_cFRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_RNA-seq_100 -z 3099922541 -n 20294129 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Intron_plus_coverage.bed` (63657)
Cumulative cfrif plot completed!
Command completed. Elapsed time: 0:00:35. Running peak memory: 5.727GB.
PID: 63657; Command: Rscript; Return code: 0; Memory used: 0.46GB
> `cFRiF` QC_hg38/K562_RNA-seq_100_cFRiF.pdf cFRiF QC_hg38/K562_RNA-seq_100_cFRiF.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_FRiF.pdf`
> `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s K562_RNA-seq_100 -z 3099922541 -n 20294129 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_Intron_plus_coverage.bed` (63701)
Cumulative frif plot completed!
Command completed. Elapsed time: 0:00:30. Running peak memory: 5.727GB.
PID: 63701; Command: Rscript; Return code: 0; Memory used: 0.442GB
> `FRiF` QC_hg38/K562_RNA-seq_100_FRiF.pdf FRiF QC_hg38/K562_RNA-seq_100_FRiF.png PEPPRO _OBJ_
### Calculate mRNA contamination (06-15 09:06:10) elapsed: 69.0 _TIME_
Missing stat 'mRNA_contamination'
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_introns_sort.bed`
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_exons_sort.bed` (63738,63739)
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.727GB.
PID: 63739; Command: bedtools; Return code: 0; Memory used: 0.086GB
PID: 63738; Command: grep; Return code: 0; Memory used: 0.004GB
> `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/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_100/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_introns_sort.bed` (63745,63746,63747)
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.727GB.
PID: 63745; Command: grep; Return code: 0; Memory used: 0.005GB
PID: 63747; Command: bedtools; Return code: 0; Memory used: 0.003GB
PID: 63746; 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_100/QC_hg38/K562_RNA-seq_100_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_introns_coverage.bed`
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_exons_coverage.bed` (63754)
Command completed. Elapsed time: 0:01:30. Running peak memory: 5.727GB.
PID: 63754; Command: bedtools; Return code: 0; Memory used: 0.22GB
> `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_sort.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_introns_coverage.bed` (63829)
Command completed. Elapsed time: 0:01:28. Running peak memory: 5.727GB.
PID: 63829; Command: bedtools; Return code: 0; Memory used: 0.206GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_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]/44.16138)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_exons_rpkm.bed` (63902,63903,63904)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.727GB.
PID: 63902; Command: awk; Return code: 0; Memory used: 0.006GB
PID: 63904; Command: sort; Return code: 0; Memory used: 0.002GB
PID: 63903; 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_100/QC_hg38/K562_RNA-seq_100_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]/44.16138)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_introns_rpkm.bed` (63907,63908,63909)
Command completed. Elapsed time: 0:00:01. Running peak memory: 5.727GB.
PID: 63907; Command: awk; Return code: 0; Memory used: 0.007GB
PID: 63909; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 63908; 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_100/QC_hg38/K562_RNA-seq_100_exon_intron_ratios.bed`
> `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_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_100/QC_hg38/K562_RNA-seq_100_exon_intron_ratios.bed` (63911,63912,63913)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 63911; Command: join; Return code: 0; Memory used: 0.001GB
PID: 63913; Command: sort; Return code: 0; Memory used: 0.004GB
PID: 63912; 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_100/QC_hg38/K562_RNA-seq_100_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` 12.77 PEPPRO _RES_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_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_100/QC_hg38/K562_RNA-seq_100_exon_intron_ratios.bed --annotate` (63919)
mRNA contamination plot completed!
Command completed. Elapsed time: 0:00:05. Running peak memory: 5.727GB.
PID: 63919; Command: Rscript; Return code: 0; Memory used: 0.316GB
> `mRNA contamination` QC_hg38/K562_RNA-seq_100_mRNA_contamination.pdf mRNA contamination QC_hg38/K562_RNA-seq_100_mRNA_contamination.png PEPPRO _OBJ_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_exon_intron_ratios.bed.gz`
> `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/QC_hg38/K562_RNA-seq_100_exon_intron_ratios.bed` (63940)
Command completed. Elapsed time: 0:00:00. Running peak memory: 5.727GB.
PID: 63940; Command: pigz; Return code: 0; Memory used: 0.003GB
### Produce bigWig files (06-15 09:09:25) elapsed: 195.0 _TIME_
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_plus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_plus.bam` (63948)
Command completed. Elapsed time: 0:00:23. Running peak memory: 5.727GB.
PID: 63948; Command: samtools; Return code: 0; Memory used: 0.009GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_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_100/signal_hg38/K562_RNA-seq_100_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 44161380.0` (63968)
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_100/aligned_hg38/K562_RNA-seq_100_plus.bam'
Temporary files will be stored in: 'tmp_K562_RNA-seq_100_plus_cuttrace_i5cpm31b'
Processing with 4 cores...
Discarding 116 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr15_KI270727v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_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_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_GL000213v1', 'chrUn_KI270747v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1']
Keeping 79 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_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_KI270726v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270738v1_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_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 79 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_plus_exact_body_0-mer.bw'
Merging 79 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_plus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:07:08. Running peak memory: 5.727GB.
PID: 63968; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.986GB
Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_minus_smooth_body_0-mer.bw`
> `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_minus.bam` (65502)
Command completed. Elapsed time: 0:00:23. Running peak memory: 5.727GB.
PID: 65502; Command: samtools; Return code: 0; Memory used: 0.008GB
> `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/aligned_hg38/K562_RNA-seq_100_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_100/signal_hg38/K562_RNA-seq_100_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 44161380.0` (65522)
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_100/aligned_hg38/K562_RNA-seq_100_minus.bam'
Temporary files will be stored in: 'tmp_K562_RNA-seq_100_minus_cuttrace_za4nvju3'
Processing with 4 cores...
Discarding 118 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr14_KI270723v1_random', 'chr17_KI270730v1_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_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_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270521v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrEBV']
Keeping 77 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', 'chr5_GL000208v1_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', 'chr22_KI270732v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270515v1', 'chrUn_KI270583v1', '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 77 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_minus_exact_body_0-mer.bw'
Merging 77 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/K562_RNA-seq_100/signal_hg38/K562_RNA-seq_100_minus_smooth_body_0-mer.bw'
Command completed. Elapsed time: 0:07:08. Running peak memory: 5.727GB.
PID: 65522; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.701GB
### Pipeline completed. Epilogue
* Elapsed time (this run): 2:07:14
* Total elapsed time (all runs): 2:42:53
* Peak memory (this run): 5.7268 GB
* Pipeline completed time: 2020-06-15 09:24:25