### Pipeline run code and environment: * Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name HEK_PRO-seq --genome hg38 --input /project/shefflab/data//guertin/fastq/SRR8608074_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --input2 /project/shefflab/data//guertin/fastq/SRR8608074_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R` * Compute host: udc-ba25-32c0 * Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc * Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/ * Pipeline started at: (06-15 07:17:12) elapsed: 0.0 _TIME_ ### Version log: * Python version: 3.6.6 * Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines` * Pipeline version: 0.9.8 * Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10 * Pipeline branch: * master * Pipeline date: 2020-06-09 11:36:49 -0400 * Pipeline diff: 40 files changed, 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/SRR8608074_PE1.fastq.gz']` * `input2`: `['/project/shefflab/data//guertin/fastq/SRR8608074_PE2.fastq.gz']` * `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`: `True` * `pre_name`: `None` * `prealignments`: `['human_rDNA']` * `prioritize`: `False` * `protocol`: `PRO` * `recover`: `True` * `sample_name`: `HEK_PRO-seq` * `scale`: `True` * `search_file`: `None` * `silent`: `False` * `single_or_paired`: `PAIRED` * `sob`: `False` * `testmode`: `False` * `trimmer`: `seqtk` * `umi_len`: `8` * `verbosity`: `None` ---------------------------------------- Local input file: /project/shefflab/data//guertin/fastq/SRR8608074_PE1.fastq.gz Local input file: /project/shefflab/data//guertin/fastq/SRR8608074_PE2.fastq.gz > `File_mb` 1337.94 PEPPRO _RES_ > `Read_type` PAIRED 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: 2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R1.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/SRR8608074_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R1.fastq.gz` (380687)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 380687; Command: ln; Return code: 0; Memory used: 0.0GB Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R1.fastq.gz' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R2.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/SRR8608074_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R2.fastq.gz` (380691)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 380691; Command: ln; Return code: 0; Memory used: 0.0GB Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R2.fastq.gz' Found .fastq.gz file Found .fastq.gz file Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2.fastq` > `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1.fastq` (380697)
Command completed. Elapsed time: 0:01:45. Running peak memory: 0.002GB. PID: 380697; Command: pigz; Return code: 0; Memory used: 0.002GB > `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2.fastq` (380803)
Command completed. Elapsed time: 0:00:59. Running peak memory: 0.002GB. PID: 380803; Command: pigz; Return code: 0; Memory used: 0.002GB > `Raw_reads` 51533198 PEPPRO _RES_ > `Fastq_reads` 51533198 PEPPRO _RES_ ['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/HEK_PRO-seq_R2.fastq.gz'] ### FASTQ processing: (06-15 07:20:20) elapsed: 187.0 _TIME_ > `cutadapt --version` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq` > `(cutadapt -j 12 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq_R1_cutadapt.txt` (381203)
Command completed. Elapsed time: 0:00:40. Running peak memory: 1.773GB. PID: 381203; Command: cutadapt; Return code: 0; Memory used: 1.773GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq` (381274,381275)
Command completed. Elapsed time: 0:00:28. Running peak memory: 1.773GB. PID: 381274; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 381275; Command: seqtk; Return code: 0; Memory used: 0.002GB Evaluating read trimming > `Trimmed_reads` 20103582 PEPPRO _RES_ > `Trim_loss_rate` 60.99 PEPPRO _RES_ Targetless command, running... > `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq` (381328)
Started analysis of HEK_PRO-seq_R1_processed.fastq Approx 5% complete for HEK_PRO-seq_R1_processed.fastq Approx 10% complete for HEK_PRO-seq_R1_processed.fastq Approx 15% complete for HEK_PRO-seq_R1_processed.fastq Approx 20% complete for HEK_PRO-seq_R1_processed.fastq Approx 25% complete for HEK_PRO-seq_R1_processed.fastq Approx 30% complete for HEK_PRO-seq_R1_processed.fastq Approx 35% complete for HEK_PRO-seq_R1_processed.fastq Approx 40% complete for HEK_PRO-seq_R1_processed.fastq Approx 45% complete for HEK_PRO-seq_R1_processed.fastq Approx 50% complete for HEK_PRO-seq_R1_processed.fastq Approx 55% complete for HEK_PRO-seq_R1_processed.fastq Approx 60% complete for HEK_PRO-seq_R1_processed.fastq Approx 65% complete for HEK_PRO-seq_R1_processed.fastq Approx 70% complete for HEK_PRO-seq_R1_processed.fastq Approx 75% complete for HEK_PRO-seq_R1_processed.fastq Approx 80% complete for HEK_PRO-seq_R1_processed.fastq Approx 85% complete for HEK_PRO-seq_R1_processed.fastq Approx 90% complete for HEK_PRO-seq_R1_processed.fastq Approx 95% complete for HEK_PRO-seq_R1_processed.fastq Analysis complete for HEK_PRO-seq_R1_processed.fastqCommand completed. Elapsed time: 0:00:42. Running peak memory: 1.773GB. PID: 381328; Command: fastqc; Return code: 0; Memory used: 0.156GB > `FastQC report r1` fastqc/HEK_PRO-seq_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_trimmed.fastq` > `seqkit rmdup --threads 12 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_noadap.fastq` (381432)
[INFO][0m 916082 duplicated records removedCommand completed. Elapsed time: 0:00:47. Running peak memory: 1.986GB. PID: 381432; Command: seqkit; Return code: 0; Memory used: 1.986GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_trimmed.fastq` (381515,381516)
Command completed. Elapsed time: 0:00:21. Running peak memory: 1.986GB. PID: 381515; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 381516; Command: seqtk; Return code: 0; Memory used: 0.002GB > `grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq_R1_cutadapt.txt | awk '{print $(NF-1)}'` > `Reads_with_adapter` 16626152.0 PEPPRO _RES_ > `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq_R1_cutadapt.txt | awk '{print $(NF-1)}'` > `awk '{sum+=$1*$2} END {printf "%.0f", sum}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq_R1_cutadapt.txt` > `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_short.fastq | awk '{print $1}'` > `Uninformative_adapter_reads` 5380555.0 PEPPRO _RES_ > `Duplicate_reads` 916082.0 PEPPRO _RES_ > `Pct_uninformative_adapter_reads` 20.8819 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/processed_R1.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/processed_R1.flag` (381619)
Command completed. Elapsed time: 0:00:00. Running peak memory: 1.986GB. PID: 381619; Command: touch; Return code: 0; Memory used: 0.0GB > `cutadapt --version` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq` > `(cutadapt -j 12 -m 10 -O 1 -a GATCGTCGGACTGTAGAACTCTGAAC /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq_R2_cutadapt.txt` (381621)
Command completed. Elapsed time: 0:01:12. Running peak memory: 1.986GB. PID: 381621; Command: cutadapt; Return code: 0; Memory used: 1.927GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq` (381919,381920)
Command completed. Elapsed time: 0:00:27. Running peak memory: 1.986GB. PID: 381919; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 381920; Command: seqtk; Return code: 0; Memory used: 0.002GB Evaluating read trimming > `Trimmed_reads` 40207164 PEPPRO _RES_ > `Trim_loss_rate` 21.98 PEPPRO _RES_ Targetless command, running... > `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq` (381983)
Started analysis of HEK_PRO-seq_R1_processed.fastq Approx 5% complete for HEK_PRO-seq_R1_processed.fastq Approx 10% complete for HEK_PRO-seq_R1_processed.fastq Approx 15% complete for HEK_PRO-seq_R1_processed.fastq Approx 20% complete for HEK_PRO-seq_R1_processed.fastq Approx 25% complete for HEK_PRO-seq_R1_processed.fastq Approx 30% complete for HEK_PRO-seq_R1_processed.fastq Approx 35% complete for HEK_PRO-seq_R1_processed.fastq Approx 40% complete for HEK_PRO-seq_R1_processed.fastq Approx 45% complete for HEK_PRO-seq_R1_processed.fastq Approx 50% complete for HEK_PRO-seq_R1_processed.fastq Approx 55% complete for HEK_PRO-seq_R1_processed.fastq Approx 60% complete for HEK_PRO-seq_R1_processed.fastq Approx 65% complete for HEK_PRO-seq_R1_processed.fastq Approx 70% complete for HEK_PRO-seq_R1_processed.fastq Approx 75% complete for HEK_PRO-seq_R1_processed.fastq Approx 80% complete for HEK_PRO-seq_R1_processed.fastq Approx 85% complete for HEK_PRO-seq_R1_processed.fastq Approx 90% complete for HEK_PRO-seq_R1_processed.fastq Approx 95% complete for HEK_PRO-seq_R1_processed.fastq Analysis complete for HEK_PRO-seq_R1_processed.fastqCommand completed. Elapsed time: 0:00:41. Running peak memory: 1.986GB. PID: 381983; Command: fastqc; Return code: 0; Memory used: 0.155GB > `FastQC report r1` fastqc/HEK_PRO-seq_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_ Targetless command, running... > `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq` (382054)
Started analysis of HEK_PRO-seq_R2_trimmed.fastq Approx 5% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 10% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 15% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 20% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 25% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 30% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 35% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 40% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 45% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 50% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 55% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 60% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 65% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 70% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 75% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 80% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 85% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 90% complete for HEK_PRO-seq_R2_trimmed.fastq Approx 95% complete for HEK_PRO-seq_R2_trimmed.fastq Analysis complete for HEK_PRO-seq_R2_trimmed.fastqCommand completed. Elapsed time: 0:00:34. Running peak memory: 1.986GB. PID: 382054; Command: fastqc; Return code: 0; Memory used: 0.153GB > `FastQC report r2` fastqc/HEK_PRO-seq_R2_trimmed_fastqc.html FastQC report r2 None PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq.histogram` > `fastq_pair -t 46379878 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_noadap.fastq` (382246)
Left paired: 20354925 Right paired: 20354925 Left single: 31120 Right single: 456238 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_noadap.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_noadap.fastq.single.fqCommand completed. Elapsed time: 0:01:42. Running peak memory: 2.441GB. PID: 382246; Command: fastq_pair; Return code: 0; Memory used: 2.441GB > `flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_noadap.fastq.paired.fq -o HEK_PRO-seq -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt` (382390)
Command completed. Elapsed time: 0:00:53. Running peak memory: 2.441GB. PID: 382390; Command: flash; Return code: 0; Memory used: 0.133GB ### Plot adapter insertion distribution (06-15 07:29:38) elapsed: 558.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq_adapter_insertion_distribution.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R adapt -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt -u 8` (382583)
Adapter insertion distribution plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 2.441GB. PID: 382583; Command: Rscript; Return code: 0; Memory used: 0.287GB > `Adapter insertion distribution` cutadapt/HEK_PRO-seq_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/HEK_PRO-seq_adapter_insertion_distribution.png PEPPRO _OBJ_ Missing stat 'Peak_adapter_insertion_size' > `awk 'NR>2 {print prev} {prev=$0}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq.hist | awk 'BEGIN{max= 0; max_len=0; len=0}{if ($2>0+max) {max=$2; len=$1}; max_len=$1} END{print len-8}'` > `Peak_adapter_insertion_size` 37 PEPPRO _RES_ Missing stat 'Degradation_ratio' ### Calculating degradation ratio (06-15 07:29:44) elapsed: 6.0 _TIME_ > `awk '{ if (($1-8) == 10) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq.hist` > `awk '{ if (($1-8) == 20) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq.hist` > `awk '{ if (($1-8) == 30) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq.hist` > `awk '{ if (($1-8) == 40) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq.hist` > `awk '(($1-8 ) <= 20 && ($1-8 ) >= 10){degradedSum += $2}; (($1-8 ) >= 30 && ($1-8) <= 40){intactSum += $2} END {if (intactSum < 1) {intactSum = 1} print degradedSum/intactSum}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/cutadapt/HEK_PRO-seq.hist` > `Degradation_ratio` 0.5783 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed_dups.fastq` > `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed_dups.fastq` (382613)
Command completed. Elapsed time: 0:00:22. Running peak memory: 2.441GB. PID: 382613; Command: cp; Return code: 0; Memory used: 0.002GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/processed_R2.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/processed_R2.flag` (382911)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.441GB. PID: 382911; Command: touch; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/repaired.flag` > `fastq_pair -t 46379878 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq` (382912)
Left paired: 20071296 Right paired: 20071296 Left single: 32287 Right single: 474552 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq.single.fqCommand completed. Elapsed time: 0:01:46. Running peak memory: 2.441GB. PID: 382912; Command: fastq_pair; Return code: 0; Memory used: 2.009GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq` (383044)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.441GB. PID: 383044; Command: mv; Return code: 0; Memory used: 0.001GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq` (383045)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.441GB. PID: 383045; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/repaired.flag` (383047)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.441GB. PID: 383047; Command: touch; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/dups_repaired.flag` > `fastq_pair -t 46379878 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed_dups.fastq` (383048)
Left paired: 19171561 Right paired: 19171561 Left single: 25508 Right single: 1374287 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed_dups.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed_dups.fastq.single.fqCommand completed. Elapsed time: 0:01:18. Running peak memory: 2.593GB. PID: 383048; Command: fastq_pair; Return code: 0; Memory used: 2.593GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_trimmed.fastq` (383175)
Command completed. Elapsed time: 0:00:01. Running peak memory: 2.593GB. PID: 383175; Command: mv; Return code: 0; Memory used: 0.001GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed_dups.fastq` (383182)
Command completed. Elapsed time: 0:00:01. Running peak memory: 2.593GB. PID: 383182; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/dups_repaired.flag` (383183)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.593GB. PID: 383183; Command: touch; Return code: 0; Memory used: 0.0GB ### Prealignments (06-15 07:33:13) elapsed: 209.0 _TIME_ Prealignment assemblies: ['human_rDNA'] ### Map to human_rDNA (06-15 07:33:13) elapsed: 0.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/human_rDNA_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/human_rDNA_bt2` (383184)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.593GB. PID: 383184; Command: mkfifo; Return code: 0; Memory used: 0.0GB File not added to cleanup: prealignments/human_rDNA_bt2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R2.fq.gz` > `perl /scratch/jps3dp/tools/databio//peppro/tools/filter_paired_fq.pl /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R2.fq` (383186)
> `(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 HEK_PRO-seq -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/human_rDNA_bt2 2>&1 > /dev/null)` not gzipping output File not added to cleanup: prealignments/human_rDNA_bt2 Missing stat 'Aligned_reads_human_rDNA' 20071296 reads; of these: 20071296 (100.00%) were unpaired; of these: 17956185 (89.46%) aligned 0 times 2115111 (10.54%) aligned exactly 1 time 0 (0.00%) aligned >1 times 10.54% overall alignment rate > `Aligned_reads_human_rDNA` 4230222.0 PEPPRO _RES_ > `Alignment_rate_human_rDNA` 10.52 PEPPRO _RES_ ### Map to human_rDNA (06-15 07:36:01) elapsed: 168.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/human_rDNA_dups_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/human_rDNA_dups_bt2` (383576)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.593GB. PID: 383576; Command: mkfifo; Return code: 0; Memory used: 0.002GB File not added to cleanup: prealignments/human_rDNA_dups_bt2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R2.fq.gz` > `perl /scratch/jps3dp/tools/databio//peppro/tools/filter_paired_fq.pl /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_dups_R2.fq` (383578)
> `(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 HEK_PRO-seq -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/fastq/HEK_PRO-seq_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)` not gzipping output 2115112 reads skipped 0 reads lost File not added to cleanup: prealignments/human_rDNA_dups_bt2 ### Map to genome (06-15 07:38:40) elapsed: 159.0 _TIME_ No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_fail_qc_dups.bam Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam` > `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id HEK_PRO-seq -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R2.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/tmp6ifjo32x -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp.bam` (383744,383745,383746)
1726816 reads skipped 0 reads lost 17956184 reads; of these: 17956184 (100.00%) were paired; of these: 5503120 (30.65%) aligned concordantly 0 times 10297215 (57.35%) aligned concordantly exactly 1 time 2155849 (12.01%) aligned concordantly >1 times ---- 5503120 pairs aligned concordantly 0 times; of these: 1505429 (27.36%) aligned discordantly 1 time ---- 3997691 pairs aligned 0 times concordantly or discordantly; of these: 7995382 mates make up the pairs; of these: 2807990 (35.12%) aligned 0 times 2063628 (25.81%) aligned exactly 1 time 3123764 (39.07%) aligned >1 times 92.18% overall alignment rate [bam_sort_core] merging from 9 files and 1 in-memory blocks...Command completed. Elapsed time: 0:33:26. Running peak memory: 3.772GB. PID: 383745; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 383744; Command: bowtie2; Return code: 0; Memory used: 3.772GB PID: 383746; Command: samtools; Return code: 0; Memory used: 0.928GB > `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam` (387133)
Command completed. Elapsed time: 0:00:51. Running peak memory: 3.772GB. PID: 387133; Command: samtools; Return code: 0; Memory used: 0.018GB > `samtools depth -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'` > `Mapped_reads` 33104378 PEPPRO _RES_ > `QC_filtered_reads` 18769818 PEPPRO _RES_ > `Aligned_reads` 14334559.5 PEPPRO _RES_ > `Alignment_rate` 35.65 PEPPRO _RES_ > `Total_efficiency` 27.82 PEPPRO _RES_ > `Read_depth` 2.41 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort_dups.bam` > `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id HEK_PRO-seq -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_dups_R2.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/tmp6ifjo32x -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp_dups.bam` (388990,388996,388997)
17444745 reads; of these: 17444745 (100.00%) were paired; of these: 5326191 (30.53%) aligned concordantly 0 times 10028868 (57.49%) aligned concordantly exactly 1 time 2089686 (11.98%) aligned concordantly >1 times ---- 5326191 pairs aligned concordantly 0 times; of these: 1467659 (27.56%) aligned discordantly 1 time ---- 3858532 pairs aligned 0 times concordantly or discordantly; of these: 7717064 mates make up the pairs; of these: 2726098 (35.33%) aligned 0 times 1998944 (25.90%) aligned exactly 1 time 2992022 (38.77%) aligned >1 times 92.19% overall alignment rate [bam_sort_core] merging from 9 files and 1 in-memory blocks...Command completed. Elapsed time: 0:30:01. Running peak memory: 3.772GB. PID: 388990; Command: bowtie2; Return code: 0; Memory used: 3.756GB PID: 388996; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 388997; Command: samtools; Return code: 0; Memory used: 0.906GB > `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort_dups.bam` (393207)
Command completed. Elapsed time: 0:00:55. Running peak memory: 3.772GB. PID: 393207; Command: samtools; Return code: 0; Memory used: 0.018GB ### Compress all unmapped read files (06-15 08:57:19) elapsed: 4719.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R1.fq.gz` > `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R1.fq` (393916)
Command completed. Elapsed time: 0:00:20. Running peak memory: 3.772GB. PID: 393916; Command: pigz; Return code: 0; Memory used: 0.011GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R2.fq.gz` > `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/prealignments/HEK_PRO-seq_human_rDNA_unmap_R2.fq` (393975)
Command completed. Elapsed time: 0:00:23. Running peak memory: 3.772GB. PID: 393975; Command: pigz; Return code: 0; Memory used: 0.013GB Missing stat 'Mitochondrial_reads' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp.bam` (394034)
Command completed. Elapsed time: 0:00:24. Running peak memory: 3.772GB. PID: 394034; Command: samtools; Return code: 0; Memory used: 0.013GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3` > `Mitochondrial_reads` 325556 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_noMT.bam` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam` (394095)
Command completed. Elapsed time: 0:00:20. Running peak memory: 3.772GB. PID: 394095; Command: samtools; Return code: 0; Memory used: 0.015GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam | cut -f 1-2 | awk '{print $1, 0, $2}' | grep -vwe 'chrM' -vwe 'chrMT' -vwe 'M' -vwe 'MT' -vwe 'rCRSd' -vwe 'rCRSd_3k' > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/chr_sizes.bed` (394141,394142,394143,394144)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 394142; Command: cut; Return code: 0; Memory used: 0.0GB PID: 394144; Command: grep; Return code: 0; Memory used: 0.0GB PID: 394141; Command: samtools; Return code: 0; Memory used: 0.009GB PID: 394143; Command: awk; Return code: 0; Memory used: 0.0GB > `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_noMT.bam` (394146)
Command completed. Elapsed time: 0:00:28. Running peak memory: 3.772GB. PID: 394146; Command: samtools; Return code: 0; Memory used: 0.019GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam` (394211)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 394211; Command: mv; Return code: 0; Memory used: 0.001GB > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam` (394213)
Command completed. Elapsed time: 0:00:20. Running peak memory: 3.772GB. PID: 394213; Command: samtools; Return code: 0; Memory used: 0.015GB ### Split BAM file (06-15 08:59:34) elapsed: 135.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam` (394562,394563)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:44. Running peak memory: 3.772GB. PID: 394562; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 394563; Command: samtools; Return code: 0; Memory used: 3.641GB > `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE2.bam` (395221,395222)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:39. Running peak memory: 3.772GB. PID: 395221; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 395222; Command: samtools; Return code: 0; Memory used: 3.076GB Missing stat 'Maximum_read_length' > `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam | grep '^SN' | cut -f 2- | grep 'maximum length:' | cut -f 2-` > `Maximum_read_length` 38 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_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp_dups.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp_dups.bam` (395571)
Command completed. Elapsed time: 0:00:23. Running peak memory: 3.772GB. PID: 395571; Command: samtools; Return code: 0; Memory used: 0.014GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp_dups.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3` Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort_dups.bam` No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort_dups.bam.bai Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_dups_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_dups_PE1.bam` (396181,396182)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:53. Running peak memory: 3.772GB. PID: 396181; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 396182; Command: samtools; Return code: 0; Memory used: 3.58GB > `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_dups_PE2.bam` (396694,396695)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:38. Running peak memory: 3.772GB. PID: 396694; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 396695; Command: samtools; Return code: 0; Memory used: 3.022GB ### Calculate library complexity (06-15 09:07:34) elapsed: 479.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_out.txt` > `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_dups_PE1.bam` (397460)
BAM_INPUT TOTAL READS = 14923343 COUNTS_SUM = 14923343 DISTINCT READS = 1.32013e+07 DISTINCT COUNTS = 220 MAX COUNT = 14762 COUNTS OF 1 = 1.216e+07 OBSERVED COUNTS (14763) 1 12160007 2 801020 3 141654 4 44209 5 19541 6 10184 7 6080 8 3969 9 2710 10 1970 11 1530 12 1137 13 864 14 760 15 571 16 491 17 498 18 370 19 342 20 262 21 230 22 212 23 195 24 181 25 170 26 146 27 128 28 114 29 96 30 109 31 85 32 81 33 65 34 71 35 68 36 72 37 52 38 39 39 48 40 40 41 41 42 27 43 34 44 29 45 27 46 38 47 28 48 36 49 36 50 21 51 18 52 24 53 12 54 23 55 15 56 18 57 21 58 15 59 18 60 8 61 14 62 16 63 11 64 8 65 8 66 10 67 10 68 11 69 12 70 12 71 5 72 6 73 10 74 5 75 8 76 10 77 5 78 8 79 8 80 5 81 7 82 4 83 5 84 6 85 6 86 3 87 5 88 5 89 4 90 2 91 4 92 6 93 4 94 6 95 5 96 9 97 3 98 6 99 2 100 2 101 4 103 3 104 2 105 4 106 1 107 2 108 3 109 2 110 5 111 4 112 7 113 2 114 3 115 2 116 1 117 1 118 1 120 2 121 2 122 4 123 1 124 1 125 1 126 5 127 2 128 1 129 1 130 3 132 4 133 4 134 2 135 1 137 2 138 1 139 3 140 2 141 2 142 2 145 1 147 2 148 5 149 1 152 2 153 1 158 1 159 1 160 1 161 2 163 1 164 1 165 1 166 1 168 2 169 1 170 1 172 2 176 1 177 1 179 1 182 1 184 2 185 2 188 1 189 1 191 3 194 1 202 1 206 2 208 1 209 2 211 1 215 2 217 1 222 1 224 1 225 3 226 2 229 1 240 2 241 1 244 1 248 1 275 1 276 1 277 1 283 1 287 1 288 1 289 1 292 1 328 1 351 1 358 1 361 1 363 1 404 1 431 2 436 1 469 1 544 1 581 1 610 1 612 1 696 1 726 1 758 1 778 1 880 1 973 1 1110 1 1493 1 1596 1 1700 1 1764 1 1771 1 2430 1 3752 1 5609 1 8568 1 14762 1 sample size: 1000000 sample size: 2000000 sample size: 3000000 sample size: 4000000 sample size: 5000000 sample size: 6000000 sample size: 7000000 sample size: 8000000 sample size: 9000000 sample size: 10000000 sample size: 11000000 sample size: 12000000 sample size: 13000000 sample size: 14000000Command completed. Elapsed time: 0:01:19. Running peak memory: 3.772GB. PID: 397460; Command: preseq; Return code: 0; Memory used: 0.005GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_yield.txt` > `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_dups_PE1.bam` (397570)
BAM_INPUT TOTAL READS = 14923343 DISTINCT READS = 1.32013e+07 DISTINCT COUNTS = 220 MAX COUNT = 14762 COUNTS OF 1 = 1.216e+07 MAX TERMS = 100 OBSERVED COUNTS (14763) 1 12160007 2 801020 3 141654 4 44209 5 19541 6 10184 7 6080 8 3969 9 2710 10 1970 11 1530 12 1137 13 864 14 760 15 571 16 491 17 498 18 370 19 342 20 262 21 230 22 212 23 195 24 181 25 170 26 146 27 128 28 114 29 96 30 109 31 85 32 81 33 65 34 71 35 68 36 72 37 52 38 39 39 48 40 40 41 41 42 27 43 34 44 29 45 27 46 38 47 28 48 36 49 36 50 21 51 18 52 24 53 12 54 23 55 15 56 18 57 21 58 15 59 18 60 8 61 14 62 16 63 11 64 8 65 8 66 10 67 10 68 11 69 12 70 12 71 5 72 6 73 10 74 5 75 8 76 10 77 5 78 8 79 8 80 5 81 7 82 4 83 5 84 6 85 6 86 3 87 5 88 5 89 4 90 2 91 4 92 6 93 4 94 6 95 5 96 9 97 3 98 6 99 2 100 2 101 4 103 3 104 2 105 4 106 1 107 2 108 3 109 2 110 5 111 4 112 7 113 2 114 3 115 2 116 1 117 1 118 1 120 2 121 2 122 4 123 1 124 1 125 1 126 5 127 2 128 1 129 1 130 3 132 4 133 4 134 2 135 1 137 2 138 1 139 3 140 2 141 2 142 2 145 1 147 2 148 5 149 1 152 2 153 1 158 1 159 1 160 1 161 2 163 1 164 1 165 1 166 1 168 2 169 1 170 1 172 2 176 1 177 1 179 1 182 1 184 2 185 2 188 1 189 1 191 3 194 1 202 1 206 2 208 1 209 2 211 1 215 2 217 1 222 1 224 1 225 3 226 2 229 1 240 2 241 1 244 1 248 1 275 1 276 1 277 1 283 1 287 1 288 1 289 1 292 1 328 1 351 1 358 1 361 1 363 1 404 1 431 2 436 1 469 1 544 1 581 1 610 1 612 1 696 1 726 1 758 1 778 1 880 1 973 1 1110 1 1493 1 1596 1 1700 1 1764 1 1771 1 2430 1 3752 1 5609 1 8568 1 14762 1 [ESTIMATING YIELD CURVE] [BOOTSTRAPPING HISTOGRAM] .................................................................................................... [COMPUTING CONFIDENCE INTERVALS] [WRITING OUTPUT]Command completed. Elapsed time: 0:01:24. Running peak memory: 3.772GB. PID: 397570; Command: preseq; Return code: 0; Memory used: 0.005GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_counts.txt` > `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_counts.txt` (397921)
Command completed. Elapsed time: 0:00:19. Running peak memory: 3.772GB. PID: 397921; Command: echo; Return code: 0; Memory used: 0.006GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_plot.png` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R preseq -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_plot` (397941)
Processing HEK_PRO-seq INFO: Found real counts for HEK_PRO-seq - Total (M): 15.183469 Unique (M): 14.923343 Library complexity plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 397941; Command: Rscript; Return code: 0; Memory used: 0.268GB > `Library complexity` QC_hg38/HEK_PRO-seq_preseq_plot.pdf Library complexity QC_hg38/HEK_PRO-seq_preseq_plot.png PEPPRO _OBJ_ Missing stat 'Frac_exp_unique_at_10M' > `grep -w '10000000' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_preseq_yield.txt | awk '{print $2}'` > `Frac_exp_unique_at_10M` 0.9099 PEPPRO _RES_ ### Calculate NRF, PBC1, and PBC2 (06-15 09:10:42) elapsed: 188.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam` (397960)
Command completed. Elapsed time: 0:00:10. Running peak memory: 3.772GB. PID: 397960; Command: samtools; Return code: 0; Memory used: 0.008GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_bamQC.tsv` > `/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_bamQC.tsv` (397979)
Configured logger 'root' using pararead v0.6 Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam' Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/tmp_HEK_PRO-seq_PE1_q52j1sna' Processing with 12 cores... Discarding 105 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270726v1_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_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270748v1', 'chrUn_KI270752v1', 'chrUn_KI270756v1'] Keeping 90 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270725v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270589v1', 'chrUn_KI270330v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']Command completed. Elapsed time: 0:00:14. Running peak memory: 3.772GB. PID: 397979; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.071GB > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_bamQC.tsv` > `NRF` 1.0 PEPPRO _RES_ > `PBC1` 7591734.5 PEPPRO _RES_ > `PBC2` 7591734.5 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_unmap.bam` > `samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_unmap.bam` (398020)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 398020; Command: samtools; Return code: 0; Memory used: 0.009GB > `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_temp.bam` > `Unmapped_reads` 2807990 PEPPRO _RES_ ### Split BAM by strand (06-15 09:11:17) elapsed: 35.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam` > `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam` (398059)
Command completed. Elapsed time: 0:00:45. Running peak memory: 3.772GB. PID: 398059; Command: samtools; Return code: 0; Memory used: 0.006GB > `samtools view -bh -f 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam` (398099)
Command completed. Elapsed time: 0:00:44. Running peak memory: 3.772GB. PID: 398099; Command: samtools; Return code: 0; Memory used: 0.006GB ### Calculate TSS enrichment (06-15 09:12:46) elapsed: 89.0 _TIME_ Missing stat 'TSS_non-coding_score' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/minus_TSS.tsv` > `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (398152)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398152; Command: sed; Return code: 0; Memory used: 0.002GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_plus_TssEnrichment.txt` > `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_plus_TssEnrichment.txt` (398154)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 398154; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.987GB > `TSS_coding_score` 16.0 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_minus_TssEnrichment.txt` > `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_minus_TssEnrichment.txt` (398185)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 398185; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.981GB > `TSS_non-coding_score` 2.4 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_TSSenrichment.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_minus_TssEnrichment.txt` (398216)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_minus_TssEnrichment.txt `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' TSS enrichment plot completed!Command completed. Elapsed time: 0:00:06. Running peak memory: 3.772GB. PID: 398216; Command: Rscript; Return code: 0; Memory used: 0.32GB > `TSS enrichment` QC_hg38/HEK_PRO-seq_TSSenrichment.pdf TSS enrichment QC_hg38/HEK_PRO-seq_TSSenrichment.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt` > `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.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/HEK_PRO-seq/QC_hg38/chr_order.txt` (398238,398239,398240,398241)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398238; Command: samtools; Return code: 0; Memory used: 0.0GB PID: 398240; Command: awk; Return code: 0; Memory used: 0.0GB PID: 398239; Command: grep; Return code: 0; Memory used: 0.0GB PID: 398241; Command: awk; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_keep.txt` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_keep.txt` (398243)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398243; Command: cut; Return code: 0; Memory used: 0.0GB ### Calculate Pause Index (PI) (06-15 09:13:03) elapsed: 17.0 _TIME_ Missing stat 'Pause_index' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_ensembl_gene_body.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_TSS.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_ensembl_tss.bed` (398245,398246)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.772GB. PID: 398245; Command: grep; Return code: 0; Memory used: 0.002GB PID: 398246; Command: bedtools; Return code: 0; Memory used: 0.099GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_gene_body.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_ensembl_gene_body.bed` (398250,398251)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398250; Command: grep; Return code: 0; Memory used: 0.003GB PID: 398251; Command: bedtools; Return code: 0; Memory used: 0.022GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_TSS_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4,4 -k7,7nr | sort -k4,4 -u > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_TSS_density.bed` (398254,398255,398256,398257)
Command completed. Elapsed time: 0:00:19. Running peak memory: 3.772GB. PID: 398254; Command: bedtools; Return code: 0; Memory used: 0.009GB PID: 398256; Command: sort; Return code: 0; Memory used: 0.012GB PID: 398255; Command: awk; Return code: 0; Memory used: 0.001GB PID: 398257; Command: sort; Return code: 0; Memory used: 0.003GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_gene_body_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_gene_body_density.bed` (398274,398275,398276)
Command completed. Elapsed time: 0:00:21. Running peak memory: 3.772GB. PID: 398274; Command: bedtools; Return code: 0; Memory used: 0.035GB PID: 398276; Command: sort; Return code: 0; Memory used: 0.006GB PID: 398275; Command: awk; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_pause_index.bed` > `join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_gene_body_density.bed | awk -v OFS=' ' '{ if ($5 == "+"){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2), ($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}' | env LC_COLLATE=C sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/tmp3fy58s0e` (398295,398296,398297)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398295; Command: join; Return code: 0; Memory used: 0.001GB PID: 398297; Command: env; Return code: 0; Memory used: 0.006GB PID: 398296; Command: awk; Return code: 0; Memory used: 0.001GB > `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/tmp3fy58s0e | 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/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_pause_index.bed` > `awk -v OFS=' ' '{ if ($5 > 0.0136883) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/tmp3fy58s0e > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_pause_index.bed` (398304)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398304; Command: awk; Return code: 0; Memory used: 0.002GB > `sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_pause_index.bed | awk ' { a[i++]=$5; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'` > `Pause_index` 10.23 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_pause_index.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R pi --annotate -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_pause_index.bed` (398309)
Pause index plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 398309; Command: Rscript; Return code: 0; Memory used: 0.316GB > `Pause index` QC_hg38/HEK_PRO-seq_pause_index.pdf Pause index QC_hg38/HEK_PRO-seq_pause_index.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_pause_index.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_pause_index.bed` (398330)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398330; Command: pigz; Return code: 0; Memory used: 0.002GB ### Calculate Fraction of Reads in pre-mature mRNA (06-15 09:13:50) elapsed: 47.0 _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/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam` 14334559.5 5618447 > `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/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam` 14334559.5 5337871 > `Minus_FRiP` 0.37 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_gene_coverage.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_gene_sort.bed` (398370,398371)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.772GB. PID: 398370; Command: grep; Return code: 0; Memory used: 0.004GB PID: 398371; Command: bedtools; Return code: 0; Memory used: 0.006GB > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_gene_coverage.bed` (398373)
Command completed. Elapsed time: 0:00:20. Running peak memory: 3.772GB. PID: 398373; Command: bedtools; Return code: 0; Memory used: 0.036GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/hg38_annotations.bed` > `ln -sf /project/shefflab/genomes/hg38/feat_annotation/default/hg38_annotations.bed.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/hg38_annotations.bed.gz` (398391)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398391; Command: ln; Return code: 0; Memory used: 0.0GB > `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/hg38_annotations.bed` (398392)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398392; Command: pigz; Return code: 0; Memory used: 0.002GB ### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 09:14:38) elapsed: 49.0 _TIME_ > `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/hg38_annotations.bed | sort -u` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Enhancer` > `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/raw/hg38_annotations.bed` (398401)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.772GB. PID: 398401; Command: awk; Return code: 0; Memory used: 0.002GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Enhancer_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Enhancer_sort.bed` (398403,398404,398405,398406)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.772GB. PID: 398403; Command: cut; Return code: 0; Memory used: 0.0GB PID: 398404; Command: grep; Return code: 0; Memory used: 0.003GB PID: 398406; Command: bedtools; Return code: 0; Memory used: 0.047GB PID: 398405; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Enhancer_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Enhancer_plus_coverage.bed` (398409)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.772GB. PID: 398409; Command: bedtools; Return code: 0; Memory used: 0.007GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Enhancer_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Enhancer_minus_coverage.bed` (398417)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.772GB. PID: 398417; Command: bedtools; Return code: 0; Memory used: 0.007GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_sort.bed` (398428,398429,398430,398431)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398428; Command: cut; Return code: 0; Memory used: 0.0GB PID: 398429; Command: grep; Return code: 0; Memory used: 0.003GB PID: 398431; Command: bedtools; Return code: 0; Memory used: 0.008GB PID: 398430; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_plus_coverage.bed` (398433)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.772GB. PID: 398433; Command: bedtools; Return code: 0; Memory used: 0.016GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_minus_coverage.bed` (398634)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.772GB. PID: 398634; Command: bedtools; Return code: 0; Memory used: 0.013GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter Flanking Region` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_Flanking_Region` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_Flanking_Region"` (398646)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398646; Command: mv; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed` (398647,398648,398649,398650)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.772GB. PID: 398647; Command: cut; Return code: 0; Memory used: 0.0GB PID: 398649; Command: cut; Return code: 0; Memory used: 0.001GB PID: 398648; Command: grep; Return code: 0; Memory used: 0.002GB PID: 398650; Command: bedtools; Return code: 0; Memory used: 0.011GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_Flanking_Region_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_Flanking_Region_plus_coverage.bed` (398653)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.772GB. PID: 398653; Command: bedtools; Return code: 0; Memory used: 0.009GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_Flanking_Region_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_Flanking_Region_minus_coverage.bed` (398662)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.772GB. PID: 398662; Command: bedtools; Return code: 0; Memory used: 0.011GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/5' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/5_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/5_UTR"` (398671)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398671; Command: mv; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/5_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/5_UTR_sort.bed` (398672,398673,398674,398675)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.772GB. PID: 398672; Command: cut; Return code: 0; Memory used: 0.0GB PID: 398673; Command: grep; Return code: 0; Memory used: 0.003GB PID: 398675; Command: bedtools; Return code: 0; Memory used: 0.01GB PID: 398674; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_5_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_5_UTR_plus_coverage.bed` (398678)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.772GB. PID: 398678; Command: bedtools; Return code: 0; Memory used: 0.008GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_5_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_5_UTR_minus_coverage.bed` (398687)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.772GB. PID: 398687; Command: bedtools; Return code: 0; Memory used: 0.009GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/3' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/3_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/3_UTR"` (398696)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398696; Command: mv; Return code: 0; Memory used: 0.002GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/3_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/3_UTR_sort.bed` (398697,398698,398699,398700)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.772GB. PID: 398697; Command: cut; Return code: 0; Memory used: 0.0GB PID: 398698; Command: grep; Return code: 0; Memory used: 0.003GB PID: 398700; Command: bedtools; Return code: 0; Memory used: 0.035GB PID: 398699; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_3_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_3_UTR_plus_coverage.bed` (398702)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.772GB. PID: 398702; Command: bedtools; Return code: 0; Memory used: 0.009GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_3_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_3_UTR_minus_coverage.bed` (398711)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.772GB. PID: 398711; Command: bedtools; Return code: 0; Memory used: 0.01GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Exon` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Exon_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Exon_sort.bed` (398721,398722,398723,398724)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.772GB. PID: 398721; Command: cut; Return code: 0; Memory used: 0.0GB PID: 398722; Command: grep; Return code: 0; Memory used: 0.004GB PID: 398724; Command: bedtools; Return code: 0; Memory used: 0.17GB PID: 398723; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Exon_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Exon_plus_coverage.bed` (398728)
Command completed. Elapsed time: 0:00:10. Running peak memory: 3.772GB. PID: 398728; Command: bedtools; Return code: 0; Memory used: 0.012GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Exon_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Exon_minus_coverage.bed` (398738)
Command completed. Elapsed time: 0:00:10. Running peak memory: 3.772GB. PID: 398738; Command: bedtools; Return code: 0; Memory used: 0.012GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Intron` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Intron_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Intron_sort.bed` (398748,398749,398750,398751)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.772GB. PID: 398748; Command: cut; Return code: 0; Memory used: 0.0GB PID: 398750; Command: cut; Return code: 0; Memory used: 0.001GB PID: 398749; Command: grep; Return code: 0; Memory used: 0.002GB PID: 398751; Command: bedtools; Return code: 0; Memory used: 0.082GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Intron_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Intron_plus_coverage.bed` (398754)
Command completed. Elapsed time: 0:00:11. Running peak memory: 3.772GB. PID: 398754; Command: bedtools; Return code: 0; Memory used: 0.019GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Intron_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Intron_minus_coverage.bed` (398766)
Command completed. Elapsed time: 0:00:10. Running peak memory: 3.772GB. PID: 398766; Command: bedtools; Return code: 0; Memory used: 0.022GB ### Plot cFRiF/FRiF (06-15 09:16:55) elapsed: 137.0 _TIME_ > `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_cFRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s HEK_PRO-seq -z 3099922541 -n 7704166 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Intron_plus_coverage.bed` (398791)
Cumulative cfrif plot completed!Command completed. Elapsed time: 0:00:34. Running peak memory: 3.772GB. PID: 398791; Command: Rscript; Return code: 0; Memory used: 0.502GB > `cFRiF` QC_hg38/HEK_PRO-seq_cFRiF.pdf cFRiF QC_hg38/HEK_PRO-seq_cFRiF.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_FRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s HEK_PRO-seq -z 3099922541 -n 7704166 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_Intron_plus_coverage.bed` (398831)
Cumulative frif plot completed!Command completed. Elapsed time: 0:00:26. Running peak memory: 3.772GB. PID: 398831; Command: Rscript; Return code: 0; Memory used: 0.472GB > `FRiF` QC_hg38/HEK_PRO-seq_FRiF.pdf FRiF QC_hg38/HEK_PRO-seq_FRiF.png PEPPRO _OBJ_ ### Calculate mRNA contamination (06-15 09:17:57) elapsed: 62.0 _TIME_ Missing stat 'mRNA_contamination' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_introns_sort.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_exons.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_exons_sort.bed` (398864,398865)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 398864; Command: grep; Return code: 0; Memory used: 0.004GB PID: 398865; Command: bedtools; Return code: 0; Memory used: 0.099GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_introns.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_introns_sort.bed` (398871,398872,398873)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 398871; Command: grep; Return code: 0; Memory used: 0.005GB PID: 398873; Command: bedtools; Return code: 0; Memory used: 0.006GB PID: 398872; Command: bedtools; Return code: 0; Memory used: 0.036GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_introns_coverage.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exons_coverage.bed` (398880)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.772GB. PID: 398880; Command: bedtools; Return code: 0; Memory used: 0.012GB > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_introns_coverage.bed` (398896)
Command completed. Elapsed time: 0:00:19. Running peak memory: 3.772GB. PID: 398896; Command: bedtools; Return code: 0; Memory used: 0.026GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exons_rpkm.bed` > `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/14.3345595)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exons_rpkm.bed` (398914,398915,398916)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.772GB. PID: 398914; Command: awk; Return code: 0; Memory used: 0.008GB PID: 398916; Command: sort; Return code: 0; Memory used: 0.002GB PID: 398915; Command: awk; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_introns_rpkm.bed` > `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/14.3345595)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_introns_rpkm.bed` (398919,398920,398921)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.772GB. PID: 398919; Command: awk; Return code: 0; Memory used: 0.007GB PID: 398921; Command: sort; Return code: 0; Memory used: 0.005GB PID: 398920; Command: awk; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exon_intron_ratios.bed` > `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exons_rpkm.bed | awk -v OFS=' ' 'NF==11 {print $7, $8, $9, $1, ($10/$5), $11}' | sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exon_intron_ratios.bed` (398923,398924,398925)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398923; Command: join; Return code: 0; Memory used: 0.001GB PID: 398925; Command: sort; Return code: 0; Memory used: 0.005GB PID: 398924; Command: awk; Return code: 0; Memory used: 0.001GB > `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exon_intron_ratios.bed | sort -n | awk ' { a[i++]=$1; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'` > `mRNA_contamination` 1.25 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_mRNA_contamination.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exon_intron_ratios.bed --annotate` (398931)
mRNA contamination plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 398931; Command: Rscript; Return code: 0; Memory used: 0.316GB > `mRNA contamination` QC_hg38/HEK_PRO-seq_mRNA_contamination.pdf mRNA contamination QC_hg38/HEK_PRO-seq_mRNA_contamination.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exon_intron_ratios.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/QC_hg38/HEK_PRO-seq_exon_intron_ratios.bed` (398952)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.772GB. PID: 398952; Command: pigz; Return code: 0; Memory used: 0.003GB ### Produce bigWig files (06-15 09:18:49) elapsed: 52.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_plus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam` (398961)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 398961; Command: samtools; Return code: 0; Memory used: 0.012GB > `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 14334559.5` (398966)
Cutting parallel chroms in half to accommodate two tracks. Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_plus.bam' Temporary files will be stored in: 'tmp_HEK_PRO-seq_plus_cuttrace_9fiv4kcf' Processing with 4 cores... Discarding 121 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_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_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', '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_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1'] Keeping 74 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_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', '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_KI270738v1_random', 'chrUn_KI270442v1', 'chrUn_KI270519v1', 'chrUn_KI270589v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 74 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_plus_exact_body_0-mer.bw' Merging 74 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_plus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:06:15. Running peak memory: 3.772GB. PID: 398966; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.405GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_minus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam` (400419)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.772GB. PID: 400419; Command: samtools; Return code: 0; Memory used: 0.012GB > `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 14334559.5` (400428)
Cutting parallel chroms in half to accommodate two tracks. Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/aligned_hg38/HEK_PRO-seq_minus.bam' Temporary files will be stored in: 'tmp_HEK_PRO-seq_minus_cuttrace_5prlm0ru' Processing with 4 cores... Discarding 117 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr5_GL000208v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270726v1_random', 'chr17_KI270730v1_random', 'chr22_KI270735v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270465v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_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_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1'] 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_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270725v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270467v1', 'chrUn_KI270438v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270589v1', 'chrUn_KI270330v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 78 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_minus_exact_body_0-mer.bw' Merging 78 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/HEK_PRO-seq/signal_hg38/HEK_PRO-seq_minus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:06:16. Running peak memory: 3.772GB. PID: 400428; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.405GB ### Pipeline completed. Epilogue * Elapsed time (this run): 2:14:20 * Total elapsed time (all runs): 3:55:34 * Peak memory (this run): 3.7719 GB * Pipeline completed time: 2020-06-15 09:31:31