### Pipeline run code and environment: * Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_50 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_50pct_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/H9_PRO-seq_50pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R` * Compute host: udc-ba27-33c1 * Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc * Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/ * Pipeline started at: (06-15 07:17:19) elapsed: 1.0 _TIME_ ### Version log: * Python version: 3.6.6 * Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines` * Pipeline version: 0.9.8 * Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10 * Pipeline branch: * master * Pipeline date: 2020-06-09 11:36:49 -0400 * Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-) ### Arguments passed to pipeline: * `TSS_name`: `None` * `adapter`: `cutadapt` * `anno_name`: `None` * `complexity`: `False` * `config_file`: `peppro.yaml` * `cores`: `12` * `coverage`: `False` * `dedup`: `seqkit` * `dirty`: `True` * `ensembl_gene_body`: `None` * `ensembl_tss`: `None` * `exon_name`: `None` * `force_follow`: `False` * `genome_assembly`: `hg38` * `input`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_50pct_PE1.fastq.gz']` * `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_50pct_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`: `H9_PRO-seq_50` * `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/H9_PRO-seq_50pct_PE1.fastq.gz Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_50pct_PE2.fastq.gz > `File_mb` 1207.83 PEPPRO _RES_ > `Read_type` PAIRED PEPPRO _RES_ > `Genome` hg38 PEPPRO _RES_ Detected PRO input ### Merge/link and fastq conversion: (06-15 07:17:20) elapsed: 1.0 _TIME_ Number of input file sets: 2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/H9_PRO-seq_50_R1.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_50pct_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/H9_PRO-seq_50_R1.fastq.gz` (420359)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 420359; Command: ln; Return code: 0; Memory used: 0.0GB Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/H9_PRO-seq_50_R1.fastq.gz' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/H9_PRO-seq_50_R2.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_50pct_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/H9_PRO-seq_50_R2.fastq.gz` (420362)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 420362; Command: ln; Return code: 0; Memory used: 0.0GB Local input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/H9_PRO-seq_50_R2.fastq.gz' Found .fastq.gz file Found .fastq.gz file Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2.fastq` > `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/H9_PRO-seq_50_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1.fastq` (420366)
Command completed. Elapsed time: 0:02:04. Running peak memory: 0.002GB. PID: 420366; 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/H9_PRO-seq_50/raw/H9_PRO-seq_50_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2.fastq` (420492)
Command completed. Elapsed time: 0:01:05. Running peak memory: 0.002GB. PID: 420492; Command: pigz; Return code: 0; Memory used: 0.002GB > `Raw_reads` 57859902 PEPPRO _RES_ > `Fastq_reads` 57859902 PEPPRO _RES_ ['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/H9_PRO-seq_50_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/H9_PRO-seq_50_R2.fastq.gz'] ### FASTQ processing: (06-15 07:21:07) elapsed: 228.0 _TIME_ > `cutadapt --version` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq` > `(cutadapt -j 12 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50_R1_cutadapt.txt` (420881)
Command completed. Elapsed time: 0:00:48. Running peak memory: 2.471GB. PID: 420881; Command: cutadapt; Return code: 0; Memory used: 2.471GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq` (420970,420971)
Command completed. Elapsed time: 0:00:23. Running peak memory: 2.471GB. PID: 420970; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 420971; Command: seqtk; Return code: 0; Memory used: 0.002GB Evaluating read trimming > `Trimmed_reads` 14164231 PEPPRO _RES_ > `Trim_loss_rate` 75.52 PEPPRO _RES_ Targetless command, running... > `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq` (421034)
Started analysis of H9_PRO-seq_50_R1_processed.fastq Approx 5% complete for H9_PRO-seq_50_R1_processed.fastq Approx 10% complete for H9_PRO-seq_50_R1_processed.fastq Approx 15% complete for H9_PRO-seq_50_R1_processed.fastq Approx 20% complete for H9_PRO-seq_50_R1_processed.fastq Approx 25% complete for H9_PRO-seq_50_R1_processed.fastq Approx 30% complete for H9_PRO-seq_50_R1_processed.fastq Approx 35% complete for H9_PRO-seq_50_R1_processed.fastq Approx 40% complete for H9_PRO-seq_50_R1_processed.fastq Approx 45% complete for H9_PRO-seq_50_R1_processed.fastq Approx 50% complete for H9_PRO-seq_50_R1_processed.fastq Approx 55% complete for H9_PRO-seq_50_R1_processed.fastq Approx 60% complete for H9_PRO-seq_50_R1_processed.fastq Approx 65% complete for H9_PRO-seq_50_R1_processed.fastq Approx 70% complete for H9_PRO-seq_50_R1_processed.fastq Approx 75% complete for H9_PRO-seq_50_R1_processed.fastq Approx 80% complete for H9_PRO-seq_50_R1_processed.fastq Approx 85% complete for H9_PRO-seq_50_R1_processed.fastq Approx 90% complete for H9_PRO-seq_50_R1_processed.fastq Approx 95% complete for H9_PRO-seq_50_R1_processed.fastq Analysis complete for H9_PRO-seq_50_R1_processed.fastqCommand completed. Elapsed time: 0:00:34. Running peak memory: 2.471GB. PID: 421034; Command: fastqc; Return code: 0; Memory used: 0.169GB > `FastQC report r1` fastqc/H9_PRO-seq_50_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_trimmed.fastq` > `seqkit rmdup --threads 12 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_noadap.fastq` (421112)
[INFO][0m 987746 duplicated records removedCommand completed. Elapsed time: 0:00:20. Running peak memory: 2.471GB. PID: 421112; Command: seqkit; Return code: 0; Memory used: 1.034GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_trimmed.fastq` (421147,421148)
Command completed. Elapsed time: 0:00:20. Running peak memory: 2.471GB. PID: 421147; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 421148; Command: seqtk; Return code: 0; Memory used: 0.002GB > `grep 'Reads with adapters:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50_R1_cutadapt.txt | awk '{print $(NF-1)}'` > `Reads_with_adapter` 22925851.0 PEPPRO _RES_ > `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50_R1_cutadapt.txt | awk '{print $(NF-1)}'` > `awk '{sum+=$1*$2} END {printf "%.0f", sum}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50_R1_cutadapt.txt` > `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_short.fastq | awk '{print $1}'` > `Uninformative_adapter_reads` 14307341.0 PEPPRO _RES_ > `Duplicate_reads` 987746.0 PEPPRO _RES_ > `Pct_uninformative_adapter_reads` 49.4551 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/processed_R1.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/processed_R1.flag` (421234)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.471GB. PID: 421234; Command: touch; Return code: 0; Memory used: 0.002GB > `cutadapt --version` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq` > `(cutadapt -j 12 -m 10 -O 1 -a GATCGTCGGACTGTAGAACTCTGAAC /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50_R2_cutadapt.txt` (421236)
Command completed. Elapsed time: 0:01:07. Running peak memory: 2.677GB. PID: 421236; Command: cutadapt; Return code: 0; Memory used: 2.677GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq` (421551,421552)
Command completed. Elapsed time: 0:00:21. Running peak memory: 2.677GB. PID: 421551; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 421552; Command: seqtk; Return code: 0; Memory used: 0.002GB Evaluating read trimming > `Trimmed_reads` 28328462 PEPPRO _RES_ > `Trim_loss_rate` 51.04 PEPPRO _RES_ Targetless command, running... > `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq` (421604)
Started analysis of H9_PRO-seq_50_R1_processed.fastq Approx 5% complete for H9_PRO-seq_50_R1_processed.fastq Approx 10% complete for H9_PRO-seq_50_R1_processed.fastq Approx 15% complete for H9_PRO-seq_50_R1_processed.fastq Approx 20% complete for H9_PRO-seq_50_R1_processed.fastq Approx 25% complete for H9_PRO-seq_50_R1_processed.fastq Approx 30% complete for H9_PRO-seq_50_R1_processed.fastq Approx 35% complete for H9_PRO-seq_50_R1_processed.fastq Approx 40% complete for H9_PRO-seq_50_R1_processed.fastq Approx 45% complete for H9_PRO-seq_50_R1_processed.fastq Approx 50% complete for H9_PRO-seq_50_R1_processed.fastq Approx 55% complete for H9_PRO-seq_50_R1_processed.fastq Approx 60% complete for H9_PRO-seq_50_R1_processed.fastq Approx 65% complete for H9_PRO-seq_50_R1_processed.fastq Approx 70% complete for H9_PRO-seq_50_R1_processed.fastq Approx 75% complete for H9_PRO-seq_50_R1_processed.fastq Approx 80% complete for H9_PRO-seq_50_R1_processed.fastq Approx 85% complete for H9_PRO-seq_50_R1_processed.fastq Approx 90% complete for H9_PRO-seq_50_R1_processed.fastq Approx 95% complete for H9_PRO-seq_50_R1_processed.fastq Analysis complete for H9_PRO-seq_50_R1_processed.fastqCommand completed. Elapsed time: 0:00:34. Running peak memory: 2.677GB. PID: 421604; Command: fastqc; Return code: 0; Memory used: 0.167GB > `FastQC report r1` fastqc/H9_PRO-seq_50_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/H9_PRO-seq_50/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq` (421679)
Started analysis of H9_PRO-seq_50_R2_trimmed.fastq Approx 5% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 10% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 15% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 20% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 25% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 30% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 35% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 40% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 45% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 50% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 55% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 60% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 65% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 70% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 75% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 80% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 85% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 90% complete for H9_PRO-seq_50_R2_trimmed.fastq Approx 95% complete for H9_PRO-seq_50_R2_trimmed.fastq Analysis complete for H9_PRO-seq_50_R2_trimmed.fastqCommand completed. Elapsed time: 0:00:29. Running peak memory: 2.677GB. PID: 421679; Command: fastqc; Return code: 0; Memory used: 0.164GB > `FastQC report r2` fastqc/H9_PRO-seq_50_R2_trimmed_fastqc.html FastQC report r2 None PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50.histogram` > `fastq_pair -t 52073911 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_noadap.fastq` (421725)
Left paired: 14521420 Right paired: 14521420 Left single: 101190 Right single: 1339977 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_noadap.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_noadap.fastq.single.fqCommand completed. Elapsed time: 0:01:46. Running peak memory: 2.677GB. PID: 421725; Command: fastq_pair; Return code: 0; Memory used: 2.334GB > `flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_noadap.fastq.paired.fq -o H9_PRO-seq_50 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt` (421900)
Command completed. Elapsed time: 0:00:28. Running peak memory: 2.677GB. PID: 421900; Command: flash; Return code: 0; Memory used: 0.116GB ### Plot adapter insertion distribution (06-15 07:28:54) elapsed: 467.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50_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/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/cutadapt -u 8` (422100)
Adapter insertion distribution plot completed!Command completed. Elapsed time: 0:00:10. Running peak memory: 2.677GB. PID: 422100; Command: Rscript; Return code: 0; Memory used: 0.116GB > `Adapter insertion distribution` cutadapt/H9_PRO-seq_50_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_50_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/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50.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` 20 PEPPRO _RES_ Missing stat 'Degradation_ratio' ### Calculating degradation ratio (06-15 07:29:04) elapsed: 10.0 _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/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50.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/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50.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/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50.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/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50.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/H9_PRO-seq_50/cutadapt/H9_PRO-seq_50.hist` > `Degradation_ratio` 1.0308 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed_dups.fastq` > `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed_dups.fastq` (422134)
Command completed. Elapsed time: 0:00:10. Running peak memory: 2.677GB. PID: 422134; Command: cp; Return code: 0; Memory used: 0.002GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/processed_R2.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/processed_R2.flag` (422144)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.677GB. PID: 422144; Command: touch; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/repaired.flag` > `fastq_pair -t 52073911 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq` (422145)
Left paired: 14052561 Right paired: 14052561 Left single: 111670 Right single: 1375764 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq.single.fqCommand completed. Elapsed time: 0:01:42. Running peak memory: 2.677GB. PID: 422145; Command: fastq_pair; Return code: 0; Memory used: 2.174GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq` (422511)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.677GB. PID: 422511; Command: mv; Return code: 0; Memory used: 0.002GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq` (422513)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.677GB. PID: 422513; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/repaired.flag` (422514)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.677GB. PID: 422514; Command: touch; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/dups_repaired.flag` > `fastq_pair -t 52073911 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed_dups.fastq` (422515)
Left paired: 13145891 Right paired: 13145891 Left single: 84515 Right single: 2282434 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed_dups.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed_dups.fastq.single.fqCommand completed. Elapsed time: 0:01:02. Running peak memory: 2.886GB. PID: 422515; Command: fastq_pair; Return code: 0; Memory used: 2.886GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_trimmed.fastq` (422760)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.886GB. PID: 422760; Command: mv; Return code: 0; Memory used: 0.001GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed_dups.fastq` (422761)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.886GB. PID: 422761; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/dups_repaired.flag` (422762)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.886GB. PID: 422762; Command: touch; Return code: 0; Memory used: 0.0GB ### Prealignments (06-15 07:32:00) elapsed: 176.0 _TIME_ Prealignment assemblies: ['human_rDNA'] ### Map to human_rDNA (06-15 07:32:00) elapsed: 0.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/human_rDNA_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/human_rDNA_bt2` (422763)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.886GB. PID: 422763; Command: mkfifo; Return code: 0; Memory used: 0.002GB File not added to cleanup: prealignments/human_rDNA_bt2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_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/H9_PRO-seq_50/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_R2.fq` (422764)
> `(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 H9_PRO-seq_50 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/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' 14052561 reads; of these: 14052561 (100.00%) were unpaired; of these: 12594922 (89.63%) aligned 0 times 1457639 (10.37%) aligned exactly 1 time 0 (0.00%) aligned >1 times 10.37% overall alignment rate > `Aligned_reads_human_rDNA` 2915278.0 PEPPRO _RES_ > `Alignment_rate_human_rDNA` 10.29 PEPPRO _RES_ ### Map to human_rDNA (06-15 07:33:34) elapsed: 94.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/human_rDNA_dups_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/human_rDNA_dups_bt2` (422862)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.886GB. PID: 422862; Command: mkfifo; Return code: 0; Memory used: 0.0GB File not added to cleanup: prealignments/human_rDNA_dups_bt2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_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/H9_PRO-seq_50/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_dups_R2.fq` (422863)
> `(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 H9_PRO-seq_50 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/fastq/H9_PRO-seq_50_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)` not gzipping output 1457639 reads skipped 0 reads lost File not added to cleanup: prealignments/human_rDNA_dups_bt2 ### Map to genome (06-15 07:35:04) elapsed: 90.0 _TIME_ No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_fail_qc_dups.bam Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam` > `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_50 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_R2.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/tmpjlrv07a_ -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp.bam` (423321,423322,423323)
1205489 reads skipped 0 reads lost 12594922 reads; of these: 12594922 (100.00%) were paired; of these: 5220321 (41.45%) aligned concordantly 0 times 6048178 (48.02%) aligned concordantly exactly 1 time 1326423 (10.53%) aligned concordantly >1 times ---- 5220321 pairs aligned concordantly 0 times; of these: 1162030 (22.26%) aligned discordantly 1 time ---- 4058291 pairs aligned 0 times concordantly or discordantly; of these: 8116582 mates make up the pairs; of these: 3332293 (41.06%) aligned 0 times 1749898 (21.56%) aligned exactly 1 time 3034391 (37.39%) aligned >1 times 86.77% overall alignment rate [bam_sort_core] merging from 7 files and 1 in-memory blocks...Command completed. Elapsed time: 0:22:26. Running peak memory: 3.768GB. PID: 423321; Command: bowtie2; Return code: 0; Memory used: 3.768GB PID: 423322; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 423323; Command: samtools; Return code: 0; Memory used: 0.898GB > `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam` (425491)
Command completed. Elapsed time: 0:00:47. Running peak memory: 3.768GB. PID: 425491; 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/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'` > `Mapped_reads` 21857551 PEPPRO _RES_ > `QC_filtered_reads` 12774487 PEPPRO _RES_ > `Aligned_reads` 9083064.0 PEPPRO _RES_ > `Alignment_rate` 32.06 PEPPRO _RES_ > `Total_efficiency` 15.7 PEPPRO _RES_ > `Read_depth` 2.31 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort_dups.bam` > `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_50 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_dups_R2.fq | samtools view -bS - -@ 1 | samtools sort - -@ 1 -T /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/tmpjlrv07a_ -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp_dups.bam` (426431,426436,426437)
11940402 reads; of these: 11940402 (100.00%) were paired; of these: 4847903 (40.60%) aligned concordantly 0 times 5829192 (48.82%) aligned concordantly exactly 1 time 1263307 (10.58%) aligned concordantly >1 times ---- 4847903 pairs aligned concordantly 0 times; of these: 1122097 (23.15%) aligned discordantly 1 time ---- 3725806 pairs aligned 0 times concordantly or discordantly; of these: 7451612 mates make up the pairs; of these: 3092419 (41.50%) aligned 0 times 1685392 (22.62%) aligned exactly 1 time 2673801 (35.88%) aligned >1 times 87.05% overall alignment rate [bam_sort_core] merging from 6 files and 1 in-memory blocks...Command completed. Elapsed time: 0:20:02. Running peak memory: 3.768GB. PID: 426431; Command: bowtie2; Return code: 0; Memory used: 3.748GB PID: 426436; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 426437; Command: samtools; Return code: 0; Memory used: 0.9GB > `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort_dups.bam` (428904)
Command completed. Elapsed time: 0:00:44. Running peak memory: 3.768GB. PID: 428904; Command: samtools; Return code: 0; Memory used: 0.018GB ### Compress all unmapped read files (06-15 08:27:18) elapsed: 3135.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_R2.fq.gz` > `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_R2.fq` (428957)
Command completed. Elapsed time: 0:00:11. Running peak memory: 3.768GB. PID: 428957; Command: pigz; Return code: 0; Memory used: 0.013GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_R1.fq.gz` > `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/prealignments/H9_PRO-seq_50_human_rDNA_unmap_R1.fq` (428980)
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.768GB. PID: 428980; Command: pigz; Return code: 0; Memory used: 0.011GB Missing stat 'Mitochondrial_reads' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp.bam` (429003)
Command completed. Elapsed time: 0:00:19. Running peak memory: 3.768GB. PID: 429003; Command: samtools; Return code: 0; Memory used: 0.016GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3` > `Mitochondrial_reads` 420662 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_noMT.bam` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam` (429024)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.768GB. PID: 429024; Command: samtools; Return code: 0; Memory used: 0.018GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam | cut -f 1-2 | awk '{print $1, 0, $2}' | grep -vwe 'chrM' -vwe 'chrMT' -vwe 'M' -vwe 'MT' -vwe 'rCRSd' -vwe 'rCRSd_3k' > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/chr_sizes.bed` (429037,429038,429039,429040)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 429039; Command: awk; Return code: 0; Memory used: 0.0GB PID: 429037; Command: samtools; Return code: 0; Memory used: 0.008GB PID: 429040; Command: grep; Return code: 0; Memory used: 0.0GB PID: 429038; Command: cut; Return code: 0; Memory used: 0.001GB > `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_noMT.bam` (429042)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.768GB. PID: 429042; Command: samtools; Return code: 0; Memory used: 0.019GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam` (429072)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 429072; Command: mv; Return code: 0; Memory used: 0.001GB > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam` (429073)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.768GB. PID: 429073; Command: samtools; Return code: 0; Memory used: 0.017GB ### Split BAM file (06-15 08:28:45) elapsed: 87.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam` (429085,429086)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:17. Running peak memory: 3.768GB. PID: 429086; Command: samtools; Return code: 0; Memory used: 2.163GB PID: 429085; Command: samtools; Return code: 0; Memory used: 0.004GB > `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE2.bam` (429467,429468)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:05. Running peak memory: 3.768GB. PID: 429468; Command: samtools; Return code: 0; Memory used: 2.05GB PID: 429467; Command: samtools; Return code: 0; Memory used: 0.004GB Missing stat 'Maximum_read_length' > `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_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/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp_dups.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp_dups.bam` (429597)
Command completed. Elapsed time: 0:00:18. Running peak memory: 3.768GB. PID: 429597; Command: samtools; Return code: 0; Memory used: 0.017GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_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/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort_dups.bam` No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort_dups.bam.bai Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_dups_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_dups_PE1.bam` (429618,429619)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:16. Running peak memory: 3.768GB. PID: 429619; Command: samtools; Return code: 0; Memory used: 2.161GB PID: 429618; Command: samtools; Return code: 0; Memory used: 0.004GB > `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_dups_PE2.bam` (429722,429723)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:05. Running peak memory: 3.768GB. PID: 429722; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 429723; Command: samtools; Return code: 0; Memory used: 2.09GB ### Calculate library complexity (06-15 08:34:16) elapsed: 330.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_out.txt` > `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_dups_PE1.bam` (429818)
BAM_INPUT TOTAL READS = 9562095 COUNTS_SUM = 9562095 DISTINCT READS = 8.19046e+06 DISTINCT COUNTS = 211 MAX COUNT = 15296 COUNTS OF 1 = 7.50584e+06 OBSERVED COUNTS (15297) 1 7505839 2 480908 3 104705 4 39936 5 19742 6 11264 7 6802 8 4520 9 3103 10 2284 11 1772 12 1265 13 1083 14 819 15 713 16 584 17 474 18 384 19 366 20 311 21 289 22 264 23 215 24 189 25 169 26 160 27 146 28 134 29 124 30 105 31 99 32 111 33 93 34 70 35 71 36 61 37 60 38 58 39 60 40 41 41 42 42 38 43 25 44 47 45 39 46 44 47 29 48 43 49 33 50 25 51 33 52 28 53 28 54 18 55 20 56 17 57 21 58 12 59 19 60 8 61 10 62 16 63 14 64 11 65 12 66 18 67 10 68 8 69 16 70 10 71 14 72 11 73 9 74 7 75 8 76 11 77 10 78 4 79 17 80 6 81 6 82 4 83 4 84 5 85 4 86 4 87 2 88 7 89 4 90 4 91 4 92 11 93 2 94 4 95 2 96 3 97 5 98 2 99 7 100 4 101 2 102 4 103 7 104 4 105 6 106 4 107 2 108 5 109 3 110 1 111 4 113 5 114 3 115 5 116 6 117 1 118 2 119 3 120 1 122 2 123 1 126 3 127 3 128 4 129 2 130 1 131 1 133 2 134 2 135 1 137 3 138 2 144 3 145 1 147 1 149 3 151 1 152 2 153 1 156 2 158 1 159 1 160 1 161 1 163 1 164 2 165 2 166 1 167 2 168 1 169 1 170 2 173 1 174 3 177 1 178 1 180 2 181 1 182 2 183 1 188 2 190 1 193 1 198 1 201 1 205 1 208 1 215 1 216 1 224 1 226 1 236 1 243 1 251 1 254 1 259 2 266 1 268 1 272 2 279 1 284 1 289 1 311 1 351 1 355 1 358 1 368 1 369 1 370 2 461 1 471 1 480 1 527 1 544 1 609 1 669 1 689 1 848 1 998 1 1010 1 1025 1 1244 1 1258 1 1353 1 1847 1 2375 1 4751 1 5746 1 7142 1 15010 1 15296 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: 9000000Command completed. Elapsed time: 0:00:52. Running peak memory: 3.768GB. PID: 429818; Command: preseq; Return code: 0; Memory used: 0.005GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_yield.txt` > `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_dups_PE1.bam` (430051)
BAM_INPUT TOTAL READS = 9562095 DISTINCT READS = 8.19046e+06 DISTINCT COUNTS = 211 MAX COUNT = 15296 COUNTS OF 1 = 7.50584e+06 MAX TERMS = 100 OBSERVED COUNTS (15297) 1 7505839 2 480908 3 104705 4 39936 5 19742 6 11264 7 6802 8 4520 9 3103 10 2284 11 1772 12 1265 13 1083 14 819 15 713 16 584 17 474 18 384 19 366 20 311 21 289 22 264 23 215 24 189 25 169 26 160 27 146 28 134 29 124 30 105 31 99 32 111 33 93 34 70 35 71 36 61 37 60 38 58 39 60 40 41 41 42 42 38 43 25 44 47 45 39 46 44 47 29 48 43 49 33 50 25 51 33 52 28 53 28 54 18 55 20 56 17 57 21 58 12 59 19 60 8 61 10 62 16 63 14 64 11 65 12 66 18 67 10 68 8 69 16 70 10 71 14 72 11 73 9 74 7 75 8 76 11 77 10 78 4 79 17 80 6 81 6 82 4 83 4 84 5 85 4 86 4 87 2 88 7 89 4 90 4 91 4 92 11 93 2 94 4 95 2 96 3 97 5 98 2 99 7 100 4 101 2 102 4 103 7 104 4 105 6 106 4 107 2 108 5 109 3 110 1 111 4 113 5 114 3 115 5 116 6 117 1 118 2 119 3 120 1 122 2 123 1 126 3 127 3 128 4 129 2 130 1 131 1 133 2 134 2 135 1 137 3 138 2 144 3 145 1 147 1 149 3 151 1 152 2 153 1 156 2 158 1 159 1 160 1 161 1 163 1 164 2 165 2 166 1 167 2 168 1 169 1 170 2 173 1 174 3 177 1 178 1 180 2 181 1 182 2 183 1 188 2 190 1 193 1 198 1 201 1 205 1 208 1 215 1 216 1 224 1 226 1 236 1 243 1 251 1 254 1 259 2 266 1 268 1 272 2 279 1 284 1 289 1 311 1 351 1 355 1 358 1 368 1 369 1 370 2 461 1 471 1 480 1 527 1 544 1 609 1 669 1 689 1 848 1 998 1 1010 1 1025 1 1244 1 1258 1 1353 1 1847 1 2375 1 4751 1 5746 1 7142 1 15010 1 15296 1 [ESTIMATING YIELD CURVE] [BOOTSTRAPPING HISTOGRAM] .................................................................................................... [COMPUTING CONFIDENCE INTERVALS] [WRITING OUTPUT]Command completed. Elapsed time: 0:00:55. Running peak memory: 3.768GB. PID: 430051; Command: preseq; Return code: 0; Memory used: 0.005GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_counts.txt` > `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_counts.txt` (430100)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.768GB. PID: 430100; Command: echo; Return code: 0; Memory used: 0.006GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_plot.png` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R preseq -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_plot` (430116)
Processing H9_PRO-seq_50 INFO: Found real counts for H9_PRO-seq_50 - Total (M): 9.741802 Unique (M): 9.562095 Library complexity plot completed!Command completed. Elapsed time: 0:00:07. Running peak memory: 3.768GB. PID: 430116; Command: Rscript; Return code: 0; Memory used: 0.125GB > `Library complexity` QC_hg38/H9_PRO-seq_50_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_50_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/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_preseq_yield.txt | awk '{print $2}'` > `Frac_exp_unique_at_10M` 0.8538 PEPPRO _RES_ ### Calculate NRF, PBC1, and PBC2 (06-15 08:36:24) elapsed: 128.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam` (430140)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.768GB. PID: 430140; Command: samtools; Return code: 0; Memory used: 0.01GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_bamQC.tsv` > `/scratch/jps3dp/tools/databio//peppro/tools/bamQC.py --silent -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_bamQC.tsv` (430148)
Configured logger 'root' using pararead v0.6 Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam' Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/tmp_H9_PRO-seq_50_PE1_oklojtws' Processing with 12 cores... Discarding 105 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_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_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', '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_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', '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_KI270745v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1'] 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_KI270718v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']Command completed. Elapsed time: 0:00:11. Running peak memory: 3.768GB. PID: 430148; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 0.973GB > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_bamQC.tsv` > `NRF` 1.0 PEPPRO _RES_ > `PBC1` 4870901.0 PEPPRO _RES_ > `PBC2` 4870901.0 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_unmap.bam` > `samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_unmap.bam` (430189)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.768GB. PID: 430189; Command: samtools; Return code: 0; Memory used: 0.016GB > `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_temp.bam` > `Unmapped_reads` 3332293 PEPPRO _RES_ ### Split BAM by strand (06-15 08:36:51) elapsed: 27.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam` > `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam` (430225)
Command completed. Elapsed time: 0:00:35. Running peak memory: 3.768GB. PID: 430225; Command: samtools; Return code: 0; Memory used: 0.006GB > `samtools view -bh -f 16 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam` (430291)
Command completed. Elapsed time: 0:00:34. Running peak memory: 3.768GB. PID: 430291; Command: samtools; Return code: 0; Memory used: 0.006GB ### Calculate TSS enrichment (06-15 08:38:00) elapsed: 69.0 _TIME_ Missing stat 'TSS_non-coding_score' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/minus_TSS.tsv` > `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (430322)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430322; Command: sed; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_plus_TssEnrichment.txt` > `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_plus_TssEnrichment.txt` (430323)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.768GB. PID: 430323; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 1.013GB > `TSS_coding_score` 33.8 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_minus_TssEnrichment.txt` > `/scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_minus_TssEnrichment.txt` (430354)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.768GB. PID: 430354; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.786GB > `TSS_non-coding_score` 12.3 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_TSSenrichment.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_minus_TssEnrichment.txt` (430384)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_minus_TssEnrichment.txt `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' TSS enrichment plot completed!Command completed. Elapsed time: 0:00:06. Running peak memory: 3.768GB. PID: 430384; Command: Rscript; Return code: 0; Memory used: 0.32GB > `TSS enrichment` QC_hg38/H9_PRO-seq_50_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_50_TSSenrichment.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt` > `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_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/H9_PRO-seq_50/QC_hg38/chr_order.txt` (430405,430407,430408,430409)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430405; Command: samtools; Return code: 0; Memory used: 0.0GB PID: 430408; Command: awk; Return code: 0; Memory used: 0.0GB PID: 430407; Command: grep; Return code: 0; Memory used: 0.0GB PID: 430409; Command: awk; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_keep.txt` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_keep.txt` (430411)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430411; Command: cut; Return code: 0; Memory used: 0.0GB ### Calculate Pause Index (PI) (06-15 08:38:14) elapsed: 14.0 _TIME_ Missing stat 'Pause_index' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_ensembl_gene_body.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_TSS.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_ensembl_tss.bed` (430413,430414)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.768GB. PID: 430413; Command: grep; Return code: 0; Memory used: 0.004GB PID: 430414; Command: bedtools; Return code: 0; Memory used: 0.096GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_gene_body.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_ensembl_gene_body.bed` (430417,430418)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430417; Command: grep; Return code: 0; Memory used: 0.003GB PID: 430418; Command: bedtools; Return code: 0; Memory used: 0.005GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_TSS_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4,4 -k7,7nr | sort -k4,4 -u > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_TSS_density.bed` (430420,430421,430422,430423)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.768GB. PID: 430423; Command: sort; Return code: 0; Memory used: 0.002GB PID: 430420; Command: bedtools; Return code: 0; Memory used: 0.006GB PID: 430422; Command: sort; Return code: 0; Memory used: 0.009GB PID: 430421; Command: awk; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_gene_body_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_gene_body_density.bed` (430437,430438,430439)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.768GB. PID: 430437; Command: bedtools; Return code: 0; Memory used: 0.063GB PID: 430439; Command: sort; Return code: 0; Memory used: 0.006GB PID: 430438; Command: awk; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_pause_index.bed` > `join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_gene_body_density.bed | awk -v OFS=' ' '{ if ($5 == "+"){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2), ($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}' | env LC_COLLATE=C sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/tmpakoc64ig` (430455,430456,430457)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430455; Command: join; Return code: 0; Memory used: 0.001GB PID: 430457; Command: env; Return code: 0; Memory used: 0.006GB PID: 430456; Command: awk; Return code: 0; Memory used: 0.001GB > `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/tmpakoc64ig | 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/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_pause_index.bed` > `awk -v OFS=' ' '{ if ($5 > 0.0104384) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/tmpakoc64ig > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_pause_index.bed` (430463)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430463; Command: awk; Return code: 0; Memory used: 0.002GB > `sort -k5,5n /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_pause_index.bed | awk ' { a[i++]=$5; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'` > `Pause_index` 33.39 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_pause_index.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R pi --annotate -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_pause_index.bed` (430468)
Pause index plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 3.768GB. PID: 430468; Command: Rscript; Return code: 0; Memory used: 0.319GB > `Pause index` QC_hg38/H9_PRO-seq_50_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_50_pause_index.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_pause_index.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_pause_index.bed` (430489)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430489; Command: pigz; Return code: 0; Memory used: 0.004GB ### Calculate Fraction of Reads in pre-mature mRNA (06-15 08:38:53) elapsed: 39.0 _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/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam` 9083064.0 3525174 > `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/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam` 9083064.0 3287581 > `Minus_FRiP` 0.36 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_gene_coverage.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_gene_sort.bed` (430522,430523)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.768GB. PID: 430522; Command: grep; Return code: 0; Memory used: 0.004GB PID: 430523; Command: bedtools; Return code: 0; Memory used: 0.005GB > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_gene_coverage.bed` (430526)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.768GB. PID: 430526; Command: bedtools; Return code: 0; Memory used: 0.063GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/hg38_annotations.bed` > `ln -sf /project/shefflab/genomes/hg38/feat_annotation/default/hg38_annotations.bed.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/hg38_annotations.bed.gz` (430541)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430541; 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/H9_PRO-seq_50/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/hg38_annotations.bed` (430542)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430542; Command: pigz; Return code: 0; Memory used: 0.002GB ### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 08:39:29) elapsed: 36.0 _TIME_ > `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/hg38_annotations.bed | sort -u` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Enhancer` > `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/raw/hg38_annotations.bed` (430551)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.768GB. PID: 430551; Command: awk; Return code: 0; Memory used: 0.002GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Enhancer_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Enhancer | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Enhancer_sort.bed` (430553,430554,430555,430556)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.768GB. PID: 430553; Command: cut; Return code: 0; Memory used: 0.0GB PID: 430554; Command: grep; Return code: 0; Memory used: 0.002GB PID: 430556; Command: bedtools; Return code: 0; Memory used: 0.013GB PID: 430555; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Enhancer_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Enhancer_plus_coverage.bed` (430558)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.768GB. PID: 430558; Command: bedtools; Return code: 0; Memory used: 0.007GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Enhancer_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Enhancer_minus_coverage.bed` (430566)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.768GB. PID: 430566; Command: bedtools; Return code: 0; Memory used: 0.009GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_sort.bed` (430573,430574,430575,430576)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430573; Command: cut; Return code: 0; Memory used: 0.0GB PID: 430574; Command: grep; Return code: 0; Memory used: 0.003GB PID: 430576; Command: bedtools; Return code: 0; Memory used: 0.009GB PID: 430575; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_plus_coverage.bed` (430578)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.768GB. PID: 430578; Command: bedtools; Return code: 0; Memory used: 0.015GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_minus_coverage.bed` (430585)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.768GB. PID: 430585; Command: bedtools; Return code: 0; Memory used: 0.012GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter Flanking Region` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_Flanking_Region` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_Flanking_Region"` (430594)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430594; Command: mv; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_Flanking_Region_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_Flanking_Region_sort.bed` (430595,430596,430597,430598)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.768GB. PID: 430595; Command: cut; Return code: 0; Memory used: 0.0GB PID: 430597; Command: cut; Return code: 0; Memory used: 0.001GB PID: 430596; Command: grep; Return code: 0; Memory used: 0.002GB PID: 430598; Command: bedtools; Return code: 0; Memory used: 0.013GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_Flanking_Region_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_Flanking_Region_plus_coverage.bed` (430601)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.768GB. PID: 430601; Command: bedtools; Return code: 0; Memory used: 0.009GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_Flanking_Region_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_Flanking_Region_minus_coverage.bed` (430867)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.768GB. PID: 430867; Command: bedtools; Return code: 0; Memory used: 0.013GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/5' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/5_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/5_UTR"` (430878)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430878; Command: mv; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/5_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/5_UTR_sort.bed` (430879,430880,430881,430882)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.768GB. PID: 430879; Command: cut; Return code: 0; Memory used: 0.0GB PID: 430880; Command: grep; Return code: 0; Memory used: 0.003GB PID: 430882; Command: bedtools; Return code: 0; Memory used: 0.03GB PID: 430881; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_5_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_5_UTR_plus_coverage.bed` (430884)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.768GB. PID: 430884; Command: bedtools; Return code: 0; Memory used: 0.008GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_5_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_5_UTR_minus_coverage.bed` (430891)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.768GB. PID: 430891; Command: bedtools; Return code: 0; Memory used: 0.009GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/3' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/3_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/3_UTR"` (430900)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 430900; Command: mv; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/3_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/3_UTR_sort.bed` (430901,430902,430903,430904)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.768GB. PID: 430901; Command: cut; Return code: 0; Memory used: 0.0GB PID: 430902; Command: grep; Return code: 0; Memory used: 0.003GB PID: 430904; Command: bedtools; Return code: 0; Memory used: 0.011GB PID: 430903; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_3_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_3_UTR_plus_coverage.bed` (430906)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.768GB. PID: 430906; Command: bedtools; Return code: 0; Memory used: 0.009GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_3_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_3_UTR_minus_coverage.bed` (430914)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.768GB. PID: 430914; Command: bedtools; Return code: 0; Memory used: 0.008GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Exon` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Exon_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Exon | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Exon_sort.bed` (430922,430923,430924,430925)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.768GB. PID: 430922; Command: cut; Return code: 0; Memory used: 0.0GB PID: 430923; Command: grep; Return code: 0; Memory used: 0.003GB PID: 430925; Command: bedtools; Return code: 0; Memory used: 0.173GB PID: 430924; Command: cut; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Exon_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Exon_plus_coverage.bed` (430929)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.768GB. PID: 430929; Command: bedtools; Return code: 0; Memory used: 0.016GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Exon_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Exon_minus_coverage.bed` (430937)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.768GB. PID: 430937; Command: bedtools; Return code: 0; Memory used: 0.012GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Intron` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Intron_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Intron | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Intron_sort.bed` (430945,430946,430947,430948)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.768GB. PID: 430945; Command: cut; Return code: 0; Memory used: 0.0GB PID: 430947; Command: cut; Return code: 0; Memory used: 0.001GB PID: 430946; Command: grep; Return code: 0; Memory used: 0.002GB PID: 430948; Command: bedtools; Return code: 0; Memory used: 0.083GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Intron_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Intron_plus_coverage.bed` (430951)
Command completed. Elapsed time: 0:00:09. Running peak memory: 3.768GB. PID: 430951; Command: bedtools; Return code: 0; Memory used: 0.02GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Intron_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Intron_minus_coverage.bed` (430960)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.768GB. PID: 430960; Command: bedtools; Return code: 0; Memory used: 0.024GB ### Plot cFRiF/FRiF (06-15 08:41:17) elapsed: 108.0 _TIME_ > `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_cFRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_50 -z 3099922541 -n 4972328 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Intron_plus_coverage.bed` (430985)
Cumulative cfrif plot completed!Command completed. Elapsed time: 0:00:33. Running peak memory: 3.768GB. PID: 430985; Command: Rscript; Return code: 0; Memory used: 0.475GB > `cFRiF` QC_hg38/H9_PRO-seq_50_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_50_cFRiF.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_FRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_50 -z 3099922541 -n 4972328 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_Intron_plus_coverage.bed` (431025)
Cumulative frif plot completed!Command completed. Elapsed time: 0:00:25. Running peak memory: 3.768GB. PID: 431025; Command: Rscript; Return code: 0; Memory used: 0.475GB > `FRiF` QC_hg38/H9_PRO-seq_50_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_50_FRiF.png PEPPRO _OBJ_ ### Calculate mRNA contamination (06-15 08:42:16) elapsed: 59.0 _TIME_ Missing stat 'mRNA_contamination' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_introns_sort.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_exons.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_exons_sort.bed` (431059,431060)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.768GB. PID: 431060; Command: bedtools; Return code: 0; Memory used: 0.098GB PID: 431059; Command: grep; Return code: 0; Memory used: 0.004GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_introns.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_introns_sort.bed` (431066,431067,431068)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.768GB. PID: 431066; Command: grep; Return code: 0; Memory used: 0.005GB PID: 431068; Command: bedtools; Return code: 0; Memory used: 0.008GB PID: 431067; Command: bedtools; Return code: 0; Memory used: 0.035GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_introns_coverage.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exons_coverage.bed` (431076)
Command completed. Elapsed time: 0:00:13. Running peak memory: 3.768GB. PID: 431076; Command: bedtools; Return code: 0; Memory used: 0.009GB > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_introns_coverage.bed` (431088)
Command completed. Elapsed time: 0:00:14. Running peak memory: 3.768GB. PID: 431088; Command: bedtools; Return code: 0; Memory used: 0.054GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exons_rpkm.bed` > `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/9.083064)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exons_rpkm.bed` (431101,431102,431103)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.768GB. PID: 431101; Command: awk; Return code: 0; Memory used: 0.007GB PID: 431103; Command: sort; Return code: 0; Memory used: 0.003GB PID: 431102; Command: awk; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_introns_rpkm.bed` > `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/9.083064)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_introns_rpkm.bed` (431105,431106,431107)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.768GB. PID: 431105; Command: awk; Return code: 0; Memory used: 0.007GB PID: 431107; Command: sort; Return code: 0; Memory used: 0.003GB PID: 431106; Command: awk; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exon_intron_ratios.bed` > `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exons_rpkm.bed | awk -v OFS=' ' 'NF==11 {print $7, $8, $9, $1, ($10/$5), $11}' | sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exon_intron_ratios.bed` (431111,431112,431113)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 431111; Command: join; Return code: 0; Memory used: 0.001GB PID: 431113; Command: sort; Return code: 0; Memory used: 0.004GB PID: 431112; Command: awk; Return code: 0; Memory used: 0.001GB > `awk '{print $5}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exon_intron_ratios.bed | sort -n | awk ' { a[i++]=$1; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'` > `mRNA_contamination` 1.29 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_mRNA_contamination.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exon_intron_ratios.bed --annotate` (431119)
mRNA contamination plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 3.768GB. PID: 431119; Command: Rscript; Return code: 0; Memory used: 0.316GB > `mRNA contamination` QC_hg38/H9_PRO-seq_50_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_50_mRNA_contamination.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exon_intron_ratios.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/QC_hg38/H9_PRO-seq_50_exon_intron_ratios.bed` (431140)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.768GB. PID: 431140; Command: pigz; Return code: 0; Memory used: 0.003GB ### Produce bigWig files (06-15 08:43:00) elapsed: 43.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_plus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam` (431148)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.768GB. PID: 431148; 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/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 9083064.0` (431152)
Cutting parallel chroms in half to accommodate two tracks. Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_plus.bam' Temporary files will be stored in: 'tmp_H9_PRO-seq_50_plus_cuttrace_q_z2c2xq' Processing with 4 cores... stdin is empty of data Discarding 123 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270710v1_random', 'chr1_KI270714v1_random', 'chr2_KI270715v1_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_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_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', '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_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1'] Keeping 72 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_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 72 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_plus_exact_body_0-mer.bw' Merging 72 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_plus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:06:15. Running peak memory: 3.768GB. PID: 431152; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.442GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_minus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam` (432469)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.768GB. PID: 432469; Command: samtools; Return code: 0; Memory used: 0.005GB > `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 9083064.0` (432473)
Cutting parallel chroms in half to accommodate two tracks. Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/aligned_hg38/H9_PRO-seq_50_minus.bam' Temporary files will be stored in: 'tmp_H9_PRO-seq_50_minus_cuttrace_5n418av4' Processing with 4 cores... stdin is empty of data Discarding 119 chunk(s) of reads: ['chrM', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr14_KI270723v1_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_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_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', '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_KI270754v1', 'chrUn_KI270755v1', 'chrUn_GL000214v1'] Keeping 76 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 76 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_minus_exact_body_0-mer.bw' Merging 76 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_50/signal_hg38/H9_PRO-seq_50_minus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:06:12. Running peak memory: 3.768GB. PID: 432473; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 3.438GB ### Pipeline completed. Epilogue * Elapsed time (this run): 1:38:18 * Total elapsed time (all runs): 2:47:09 * Peak memory (this run): 3.7684 GB * Pipeline completed time: 2020-06-15 08:55:36