### Pipeline run code and environment: * Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_100 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_100pct_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_100pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R` * Compute host: udc-ba26-35c0 * Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc * Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/ * Pipeline started at: (06-15 07:17:27) elapsed: 2.0 _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_100pct_PE1.fastq.gz']` * `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_100pct_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_100` * `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_100pct_PE1.fastq.gz Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_100pct_PE2.fastq.gz > `File_mb` 2754.18 PEPPRO _RES_ > `Read_type` PAIRED PEPPRO _RES_ > `Genome` hg38 PEPPRO _RES_ Detected PRO input ### Merge/link and fastq conversion: (06-15 07:17:28) elapsed: 2.0 _TIME_ Number of input file sets: 2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/H9_PRO-seq_100_R1.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_100pct_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/H9_PRO-seq_100_R1.fastq.gz` (217616)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 217616; 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_100/raw/H9_PRO-seq_100_R1.fastq.gz' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/H9_PRO-seq_100_R2.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_100pct_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/H9_PRO-seq_100_R2.fastq.gz` (217625)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 217625; 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_100/raw/H9_PRO-seq_100_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_100/fastq/H9_PRO-seq_100_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2.fastq` > `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/H9_PRO-seq_100_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1.fastq` (217628)
Command completed. Elapsed time: 0:04:58. Running peak memory: 0.002GB. PID: 217628; 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_100/raw/H9_PRO-seq_100_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2.fastq` (31759)
Command completed. Elapsed time: 0:01:27. Running peak memory: 0.003GB. PID: 31759; Command: pigz; Return code: 0; Memory used: 0.003GB > `Raw_reads` 115714026 PEPPRO _RES_ > `Fastq_reads` 115714026 PEPPRO _RES_ ['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/H9_PRO-seq_100_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/H9_PRO-seq_100_R2.fastq.gz'] ### FASTQ processing: (06-15 07:29:26) elapsed: 717.0 _TIME_ > `cutadapt --version` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_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_100/fastq/H9_PRO-seq_100_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/cutadapt/H9_PRO-seq_100_R1_cutadapt.txt` (332817)
Command completed. Elapsed time: 0:02:27. Running peak memory: 3.241GB. PID: 332817; Command: cutadapt; Return code: 0; Memory used: 3.241GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq` (333292,333293)
Command completed. Elapsed time: 0:01:03. Running peak memory: 3.241GB. PID: 333293; Command: seqtk; Return code: 0; Memory used: 0.002GB PID: 333292; Command: seqtk; Return code: 0; Memory used: 0.001GB Evaluating read trimming > `Trimmed_reads` 28329255 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_100/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq` (333401)
Started analysis of H9_PRO-seq_100_R1_processed.fastq Approx 5% complete for H9_PRO-seq_100_R1_processed.fastq Approx 10% complete for H9_PRO-seq_100_R1_processed.fastq Approx 15% complete for H9_PRO-seq_100_R1_processed.fastq Approx 20% complete for H9_PRO-seq_100_R1_processed.fastq Approx 25% complete for H9_PRO-seq_100_R1_processed.fastq Approx 30% complete for H9_PRO-seq_100_R1_processed.fastq Approx 35% complete for H9_PRO-seq_100_R1_processed.fastq Approx 40% complete for H9_PRO-seq_100_R1_processed.fastq Approx 45% complete for H9_PRO-seq_100_R1_processed.fastq Approx 50% complete for H9_PRO-seq_100_R1_processed.fastq Approx 55% complete for H9_PRO-seq_100_R1_processed.fastq Approx 60% complete for H9_PRO-seq_100_R1_processed.fastq Approx 65% complete for H9_PRO-seq_100_R1_processed.fastq Approx 70% complete for H9_PRO-seq_100_R1_processed.fastq Approx 75% complete for H9_PRO-seq_100_R1_processed.fastq Approx 80% complete for H9_PRO-seq_100_R1_processed.fastq Approx 85% complete for H9_PRO-seq_100_R1_processed.fastq Approx 90% complete for H9_PRO-seq_100_R1_processed.fastq Approx 95% complete for H9_PRO-seq_100_R1_processed.fastq Analysis complete for H9_PRO-seq_100_R1_processed.fastqCommand completed. Elapsed time: 0:00:58. Running peak memory: 3.241GB. PID: 333401; Command: fastqc; Return code: 0; Memory used: 0.181GB > `FastQC report r1` fastqc/H9_PRO-seq_100_R1_processed_fastqc.html FastQC report r1 None PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_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_100/fastq/H9_PRO-seq_100_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_noadap.fastq` (333478)
[INFO][0m 3047417 duplicated records removedCommand completed. Elapsed time: 0:01:14. Running peak memory: 3.241GB. PID: 333478; Command: seqkit; Return code: 0; Memory used: 2.015GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_trimmed.fastq` (333778,333779)
Command completed. Elapsed time: 0:00:53. Running peak memory: 3.241GB. PID: 333778; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 333779; 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_100/cutadapt/H9_PRO-seq_100_R1_cutadapt.txt | awk '{print $(NF-1)}'` > `Reads_with_adapter` 45847892.0 PEPPRO _RES_ > `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/cutadapt/H9_PRO-seq_100_R1_cutadapt.txt | awk '{print $(NF-1)}'` > `awk '{sum+=$1*$2} END {printf "%.0f", sum}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/cutadapt/H9_PRO-seq_100_R1_cutadapt.txt` > `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_short.fastq | awk '{print $1}'` > `Uninformative_adapter_reads` 28610139.0 PEPPRO _RES_ > `Duplicate_reads` 3047417.0 PEPPRO _RES_ > `Pct_uninformative_adapter_reads` 49.4497 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/processed_R1.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/processed_R1.flag` (333967)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.241GB. PID: 333967; Command: touch; Return code: 0; Memory used: 0.0GB > `cutadapt --version` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_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_100/fastq/H9_PRO-seq_100_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/cutadapt/H9_PRO-seq_100_R2_cutadapt.txt` (333969)
Command completed. Elapsed time: 0:01:07. Running peak memory: 3.372GB. PID: 333969; Command: cutadapt; Return code: 0; Memory used: 3.372GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed.fastq` (334088,334090)
Command completed. Elapsed time: 0:00:32. Running peak memory: 3.372GB. PID: 334088; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 334090; Command: seqtk; Return code: 0; Memory used: 0.002GB Evaluating read trimming > `Trimmed_reads` 56658510 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_100/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq` (334182)
Started analysis of H9_PRO-seq_100_R1_processed.fastq Approx 5% complete for H9_PRO-seq_100_R1_processed.fastq Approx 10% complete for H9_PRO-seq_100_R1_processed.fastq Approx 15% complete for H9_PRO-seq_100_R1_processed.fastq Approx 20% complete for H9_PRO-seq_100_R1_processed.fastq Approx 25% complete for H9_PRO-seq_100_R1_processed.fastq Approx 30% complete for H9_PRO-seq_100_R1_processed.fastq Approx 35% complete for H9_PRO-seq_100_R1_processed.fastq Approx 40% complete for H9_PRO-seq_100_R1_processed.fastq Approx 45% complete for H9_PRO-seq_100_R1_processed.fastq Approx 50% complete for H9_PRO-seq_100_R1_processed.fastq Approx 55% complete for H9_PRO-seq_100_R1_processed.fastq Approx 60% complete for H9_PRO-seq_100_R1_processed.fastq Approx 65% complete for H9_PRO-seq_100_R1_processed.fastq Approx 70% complete for H9_PRO-seq_100_R1_processed.fastq Approx 75% complete for H9_PRO-seq_100_R1_processed.fastq Approx 80% complete for H9_PRO-seq_100_R1_processed.fastq Approx 85% complete for H9_PRO-seq_100_R1_processed.fastq Approx 90% complete for H9_PRO-seq_100_R1_processed.fastq Approx 95% complete for H9_PRO-seq_100_R1_processed.fastq Analysis complete for H9_PRO-seq_100_R1_processed.fastqCommand completed. Elapsed time: 0:00:56. Running peak memory: 3.372GB. PID: 334182; Command: fastqc; Return code: 0; Memory used: 0.18GB > `FastQC report r1` fastqc/H9_PRO-seq_100_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_100/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed.fastq` (334482)
Started analysis of H9_PRO-seq_100_R2_trimmed.fastq Approx 5% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 10% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 15% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 20% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 25% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 30% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 35% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 40% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 45% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 50% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 55% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 60% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 65% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 70% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 75% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 80% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 85% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 90% complete for H9_PRO-seq_100_R2_trimmed.fastq Approx 95% complete for H9_PRO-seq_100_R2_trimmed.fastq Analysis complete for H9_PRO-seq_100_R2_trimmed.fastqCommand completed. Elapsed time: 0:01:22. Running peak memory: 3.372GB. PID: 334482; Command: fastqc; Return code: 0; Memory used: 0.165GB > `FastQC report r2` fastqc/H9_PRO-seq_100_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_100/cutadapt/H9_PRO-seq_100.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/cutadapt/H9_PRO-seq_100.histogram` > `fastq_pair -t 104142623 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_noadap.fastq` (334722)
Left paired: 29044502 Right paired: 29044502 Left single: 202372 Right single: 2678154 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_noadap.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_noadap.fastq.single.fqCommand completed. Elapsed time: 0:04:50. Running peak memory: 6.567GB. PID: 334722; Command: fastq_pair; Return code: 0; Memory used: 6.567GB > `flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_noadap.fastq.paired.fq -o H9_PRO-seq_100 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/cutadapt` (335384)
Command completed. Elapsed time: 0:01:06. Running peak memory: 6.567GB. PID: 335384; Command: flash; Return code: 0; Memory used: 0.129GB ### Plot adapter insertion distribution (06-15 07:47:54) elapsed: 1108.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/cutadapt/H9_PRO-seq_100_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_100/cutadapt/H9_PRO-seq_100.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/cutadapt -u 8` (335585)
Adapter insertion distribution plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 6.567GB. PID: 335585; Command: Rscript; Return code: 0; Memory used: 0.317GB > `Adapter insertion distribution` cutadapt/H9_PRO-seq_100_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_100_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_100/cutadapt/H9_PRO-seq_100.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 07:47:59) elapsed: 5.0 _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_100/cutadapt/H9_PRO-seq_100.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_100/cutadapt/H9_PRO-seq_100.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_100/cutadapt/H9_PRO-seq_100.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_100/cutadapt/H9_PRO-seq_100.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_100/cutadapt/H9_PRO-seq_100.hist` > `Degradation_ratio` 1.0321 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed_dups.fastq` > `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed_dups.fastq` (335614)
Command completed. Elapsed time: 0:00:27. Running peak memory: 6.567GB. PID: 335614; 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_100/fastq/processed_R2.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/processed_R2.flag` (335642)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 335642; 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_100/fastq/repaired.flag` > `fastq_pair -t 104142623 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed.fastq` (335643)
Left paired: 28105674 Right paired: 28105674 Left single: 223581 Right single: 2750162 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed.fastq.single.fqCommand completed. Elapsed time: 0:03:32. Running peak memory: 6.567GB. PID: 335643; Command: fastq_pair; Return code: 0; Memory used: 6.397GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq` (336095)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 336095; Command: mv; Return code: 0; Memory used: 0.002GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed.fastq` (336097)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 336097; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/repaired.flag` (336098)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 336098; 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_100/fastq/dups_repaired.flag` > `fastq_pair -t 104142623 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed_dups.fastq` (336099)
Left paired: 25286654 Right paired: 25286654 Left single: 163446 Right single: 5569182 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed_dups.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed_dups.fastq.single.fqCommand completed. Elapsed time: 0:02:14. Running peak memory: 6.567GB. PID: 336099; Command: fastq_pair; Return code: 0; Memory used: 5.913GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_trimmed.fastq` (336234)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 336234; Command: mv; Return code: 0; Memory used: 0.002GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed_dups.fastq` (336236)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 336236; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/dups_repaired.flag` (336237)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 336237; Command: touch; Return code: 0; Memory used: 0.0GB ### Prealignments (06-15 07:54:14) elapsed: 375.0 _TIME_ Prealignment assemblies: ['human_rDNA'] ### Map to human_rDNA (06-15 07:54:14) elapsed: 0.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/human_rDNA_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/human_rDNA_bt2` (336238)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 336238; Command: mkfifo; Return code: 0; Memory used: 0.0GB File not added to cleanup: prealignments/human_rDNA_bt2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_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_100/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_R2.fq` (336239)
> `(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_100 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/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' 28105674 reads; of these: 28105674 (100.00%) were unpaired; of these: 25192086 (89.63%) aligned 0 times 2913588 (10.37%) aligned exactly 1 time 0 (0.00%) aligned >1 times 10.37% overall alignment rate > `Aligned_reads_human_rDNA` 5827176.0 PEPPRO _RES_ > `Alignment_rate_human_rDNA` 10.28 PEPPRO _RES_ ### Map to human_rDNA (06-15 07:57:34) elapsed: 200.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/human_rDNA_dups_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/human_rDNA_dups_bt2` (336633)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 336633; Command: mkfifo; Return code: 0; Memory used: 0.002GB File not added to cleanup: prealignments/human_rDNA_dups_bt2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_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_100/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_dups_R2.fq` (336634)
> `(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_100 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/fastq/H9_PRO-seq_100_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)` not gzipping output 2913588 reads skipped 0 reads lost File not added to cleanup: prealignments/human_rDNA_dups_bt2 ### Map to genome (06-15 08:00:43) elapsed: 190.0 _TIME_ No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_fail_qc_dups.bam Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort.bam` > `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_100 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_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_100/aligned_hg38/tmpob3imm5z -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp.bam` (337074,337075,337076)
2252266 reads skipped 0 reads lost 25192086 reads; of these: 25192086 (100.00%) were paired; of these: 10443566 (41.46%) aligned concordantly 0 times 12095912 (48.01%) aligned concordantly exactly 1 time 2652608 (10.53%) aligned concordantly >1 times ---- 10443566 pairs aligned concordantly 0 times; of these: 2323449 (22.25%) aligned discordantly 1 time ---- 8120117 pairs aligned 0 times concordantly or discordantly; of these: 16240234 mates make up the pairs; of these: 6664276 (41.04%) aligned 0 times 3498753 (21.54%) aligned exactly 1 time 6077205 (37.42%) aligned >1 times 86.77% overall alignment rate [bam_sort_core] merging from 14 files and 1 in-memory blocks...Command completed. Elapsed time: 0:47:33. Running peak memory: 6.567GB. PID: 337074; Command: bowtie2; Return code: 0; Memory used: 3.777GB PID: 337075; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 337076; Command: samtools; Return code: 0; Memory used: 0.899GB > `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort.bam` (341719)
Command completed. Elapsed time: 0:01:23. Running peak memory: 6.567GB. PID: 341719; 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_100/aligned_hg38/H9_PRO-seq_100_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'` > `Mapped_reads` 43719896 PEPPRO _RES_ > `QC_filtered_reads` 25554169 PEPPRO _RES_ > `Aligned_reads` 18165727.0 PEPPRO _RES_ > `Alignment_rate` 32.06 PEPPRO _RES_ > `Total_efficiency` 15.7 PEPPRO _RES_ > `Read_depth` 3.11 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort_dups.bam` > `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_100 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_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_100/aligned_hg38/tmpob3imm5z -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp_dups.bam` (343136,343137,343138)
23034388 reads; of these: 23034388 (100.00%) were paired; of these: 9342849 (40.56%) aligned concordantly 0 times 11259901 (48.88%) aligned concordantly exactly 1 time 2431638 (10.56%) aligned concordantly >1 times ---- 9342849 pairs aligned concordantly 0 times; of these: 2170368 (23.23%) aligned discordantly 1 time ---- 7172481 pairs aligned 0 times concordantly or discordantly; of these: 14344962 mates make up the pairs; of these: 6003927 (41.85%) aligned 0 times 3261117 (22.73%) aligned exactly 1 time 5079918 (35.41%) aligned >1 times 86.97% overall alignment rate [bam_sort_core] merging from 13 files and 1 in-memory blocks...Command completed. Elapsed time: 0:42:08. Running peak memory: 6.567GB. PID: 343136; Command: bowtie2; Return code: 0; Memory used: 3.763GB PID: 343137; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 343138; Command: samtools; Return code: 0; Memory used: 0.976GB > `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort_dups.bam` (347997)
Command completed. Elapsed time: 0:01:17. Running peak memory: 6.567GB. PID: 347997; Command: samtools; Return code: 0; Memory used: 0.018GB ### Compress all unmapped read files (06-15 09:45:05) elapsed: 6261.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_R2.fq.gz` > `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_R2.fq` (348863)
Command completed. Elapsed time: 0:00:20. Running peak memory: 6.567GB. PID: 348863; Command: pigz; Return code: 0; Memory used: 0.011GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_R1.fq.gz` > `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/prealignments/H9_PRO-seq_100_human_rDNA_unmap_R1.fq` (348904)
Command completed. Elapsed time: 0:00:23. Running peak memory: 6.567GB. PID: 348904; Command: pigz; Return code: 0; Memory used: 0.013GB Missing stat 'Mitochondrial_reads' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp.bam` (348954)
Command completed. Elapsed time: 0:00:36. Running peak memory: 6.567GB. PID: 348954; Command: samtools; Return code: 0; Memory used: 0.01GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3` > `Mitochondrial_reads` 840435 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_noMT.bam` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort.bam` (348991)
Command completed. Elapsed time: 0:00:27. Running peak memory: 6.567GB. PID: 348991; Command: samtools; Return code: 0; Memory used: 0.012GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort.bam | cut -f 1-2 | awk '{print $1, 0, $2}' | grep -vwe 'chrM' -vwe 'chrMT' -vwe 'M' -vwe 'MT' -vwe 'rCRSd' -vwe 'rCRSd_3k' > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/chr_sizes.bed` (349042,349043,349044,349045)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 349044; Command: awk; Return code: 0; Memory used: 0.0GB PID: 349042; Command: samtools; Return code: 0; Memory used: 0.008GB PID: 349045; Command: grep; Return code: 0; Memory used: 0.0GB PID: 349043; 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_100/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_noMT.bam` (349047)
Command completed. Elapsed time: 0:00:33. Running peak memory: 6.567GB. PID: 349047; Command: samtools; Return code: 0; Memory used: 0.019GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort.bam` (349090)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 349090; Command: mv; Return code: 0; Memory used: 0.001GB > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort.bam` (349091)
Command completed. Elapsed time: 0:00:27. Running peak memory: 6.567GB. PID: 349091; Command: samtools; Return code: 0; Memory used: 0.012GB ### Split BAM file (06-15 09:47:50) elapsed: 165.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam` (349123,349124)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:02:32. Running peak memory: 6.567GB. PID: 349123; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 349124; Command: samtools; Return code: 0; Memory used: 5.207GB > `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE2.bam` (349708,349709)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:02:02. Running peak memory: 6.567GB. PID: 349708; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 349709; Command: samtools; Return code: 0; Memory used: 4.168GB Missing stat 'Maximum_read_length' > `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_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_100/aligned_hg38/H9_PRO-seq_100_temp_dups.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp_dups.bam` (350532)
Command completed. Elapsed time: 0:00:31. Running peak memory: 6.567GB. PID: 350532; Command: samtools; Return code: 0; Memory used: 0.012GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_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_100/aligned_hg38/H9_PRO-seq_100_sort_dups.bam` No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort_dups.bam.bai Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_dups_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_dups_PE1.bam` (350567,350568)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:02:24. Running peak memory: 6.567GB. PID: 350568; Command: samtools; Return code: 0; Memory used: 4.569GB PID: 350567; 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_100/aligned_hg38/H9_PRO-seq_100_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_dups_PE2.bam` (351036,351037)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:58. Running peak memory: 6.567GB. PID: 351036; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 351037; Command: samtools; Return code: 0; Memory used: 3.953GB ### Calculate library complexity (06-15 09:58:07) elapsed: 618.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_preseq_out.txt` > `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_dups_PE1.bam` (351323)
BAM_INPUT TOTAL READS = 18471612 COUNTS_SUM = 18471612 DISTINCT READS = 1.4838e+07 DISTINCT COUNTS = 324 MAX COUNT = 27760 COUNTS OF 1 = 1.31407e+07 OBSERVED COUNTS (27761) 1 13140744 2 1146563 3 271114 4 106759 5 54977 6 32098 7 20377 8 13755 9 9695 10 7243 11 5405 12 4178 13 3366 14 2630 15 2184 16 1670 17 1556 18 1258 19 1062 20 922 21 848 22 719 23 630 24 559 25 515 26 451 27 428 28 367 29 288 30 299 31 270 32 267 33 217 34 243 35 187 36 184 37 185 38 182 39 115 40 118 41 128 42 138 43 109 44 108 45 116 46 94 47 93 48 89 49 86 50 74 51 68 52 83 53 92 54 70 55 66 56 62 57 55 58 57 59 51 60 52 61 61 62 42 63 45 64 39 65 35 66 29 67 50 68 36 69 25 70 39 71 35 72 28 73 31 74 32 75 27 76 27 77 24 78 27 79 28 80 21 81 23 82 16 83 21 84 29 85 23 86 16 87 19 88 19 89 17 90 12 91 10 92 17 93 11 94 17 95 10 96 17 97 22 98 19 99 17 100 9 101 14 102 19 103 10 104 8 105 9 106 9 107 16 108 8 109 8 110 5 111 8 112 5 113 13 114 12 115 8 116 12 117 7 118 4 119 9 120 7 121 6 122 5 123 11 124 8 125 2 126 5 127 5 128 7 129 6 130 4 131 5 132 6 133 5 134 4 135 2 136 3 137 4 138 11 139 5 140 9 141 3 142 2 143 5 144 5 145 4 146 2 147 6 148 2 149 5 150 5 151 2 152 4 153 3 154 3 155 4 156 5 157 4 158 5 159 1 160 3 161 4 162 6 163 5 164 2 165 5 166 6 167 1 168 1 169 2 170 2 171 3 172 3 173 1 174 3 175 2 176 1 177 5 178 2 179 3 180 2 181 4 183 1 184 2 186 3 187 1 188 1 190 3 192 4 194 4 196 3 197 2 198 3 199 2 200 3 201 2 202 1 203 1 204 4 206 1 207 4 208 4 210 3 212 3 213 3 215 2 219 1 220 3 221 2 222 2 223 1 224 2 225 3 226 3 228 1 230 1 232 1 233 2 234 1 235 2 236 2 238 2 240 1 242 2 244 2 246 1 249 1 253 2 255 1 256 1 257 1 258 2 259 2 261 1 263 2 265 1 268 1 269 2 270 1 273 1 277 1 279 1 282 1 283 1 284 1 290 1 292 1 299 1 302 2 303 1 306 1 307 1 310 1 311 1 312 1 314 1 315 1 317 1 318 1 319 2 320 1 321 1 322 1 325 1 328 2 331 1 335 2 338 1 341 1 345 1 350 1 355 1 360 2 370 1 373 1 374 1 390 2 391 1 394 1 397 1 412 1 415 1 426 1 429 1 442 1 444 1 452 1 488 1 494 2 502 1 505 1 509 1 515 1 549 2 551 1 584 1 694 1 701 1 703 1 708 1 710 1 712 1 714 1 809 1 881 1 918 1 962 1 1001 1 1158 1 1264 1 1324 1 1628 1 1848 1 1890 1 1899 1 2227 1 2457 1 2584 1 3405 1 4384 1 9005 1 10491 1 13480 1 23174 1 27760 1 sample size: 1000000 sample size: 2000000 sample size: 3000000 sample size: 4000000 sample size: 5000000 sample size: 6000000 sample size: 7000000 sample size: 8000000 sample size: 9000000 sample size: 10000000 sample size: 11000000 sample size: 12000000 sample size: 13000000 sample size: 14000000 sample size: 15000000 sample size: 16000000 sample size: 17000000 sample size: 18000000Command completed. Elapsed time: 0:01:33. Running peak memory: 6.567GB. PID: 351323; 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_100/QC_hg38/H9_PRO-seq_100_preseq_yield.txt` > `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_dups_PE1.bam` (351439)
BAM_INPUT TOTAL READS = 18471612 DISTINCT READS = 1.4838e+07 DISTINCT COUNTS = 324 MAX COUNT = 27760 COUNTS OF 1 = 1.31407e+07 MAX TERMS = 100 OBSERVED COUNTS (27761) 1 13140744 2 1146563 3 271114 4 106759 5 54977 6 32098 7 20377 8 13755 9 9695 10 7243 11 5405 12 4178 13 3366 14 2630 15 2184 16 1670 17 1556 18 1258 19 1062 20 922 21 848 22 719 23 630 24 559 25 515 26 451 27 428 28 367 29 288 30 299 31 270 32 267 33 217 34 243 35 187 36 184 37 185 38 182 39 115 40 118 41 128 42 138 43 109 44 108 45 116 46 94 47 93 48 89 49 86 50 74 51 68 52 83 53 92 54 70 55 66 56 62 57 55 58 57 59 51 60 52 61 61 62 42 63 45 64 39 65 35 66 29 67 50 68 36 69 25 70 39 71 35 72 28 73 31 74 32 75 27 76 27 77 24 78 27 79 28 80 21 81 23 82 16 83 21 84 29 85 23 86 16 87 19 88 19 89 17 90 12 91 10 92 17 93 11 94 17 95 10 96 17 97 22 98 19 99 17 100 9 101 14 102 19 103 10 104 8 105 9 106 9 107 16 108 8 109 8 110 5 111 8 112 5 113 13 114 12 115 8 116 12 117 7 118 4 119 9 120 7 121 6 122 5 123 11 124 8 125 2 126 5 127 5 128 7 129 6 130 4 131 5 132 6 133 5 134 4 135 2 136 3 137 4 138 11 139 5 140 9 141 3 142 2 143 5 144 5 145 4 146 2 147 6 148 2 149 5 150 5 151 2 152 4 153 3 154 3 155 4 156 5 157 4 158 5 159 1 160 3 161 4 162 6 163 5 164 2 165 5 166 6 167 1 168 1 169 2 170 2 171 3 172 3 173 1 174 3 175 2 176 1 177 5 178 2 179 3 180 2 181 4 183 1 184 2 186 3 187 1 188 1 190 3 192 4 194 4 196 3 197 2 198 3 199 2 200 3 201 2 202 1 203 1 204 4 206 1 207 4 208 4 210 3 212 3 213 3 215 2 219 1 220 3 221 2 222 2 223 1 224 2 225 3 226 3 228 1 230 1 232 1 233 2 234 1 235 2 236 2 238 2 240 1 242 2 244 2 246 1 249 1 253 2 255 1 256 1 257 1 258 2 259 2 261 1 263 2 265 1 268 1 269 2 270 1 273 1 277 1 279 1 282 1 283 1 284 1 290 1 292 1 299 1 302 2 303 1 306 1 307 1 310 1 311 1 312 1 314 1 315 1 317 1 318 1 319 2 320 1 321 1 322 1 325 1 328 2 331 1 335 2 338 1 341 1 345 1 350 1 355 1 360 2 370 1 373 1 374 1 390 2 391 1 394 1 397 1 412 1 415 1 426 1 429 1 442 1 444 1 452 1 488 1 494 2 502 1 505 1 509 1 515 1 549 2 551 1 584 1 694 1 701 1 703 1 708 1 710 1 712 1 714 1 809 1 881 1 918 1 962 1 1001 1 1158 1 1264 1 1324 1 1628 1 1848 1 1890 1 1899 1 2227 1 2457 1 2584 1 3405 1 4384 1 9005 1 10491 1 13480 1 23174 1 27760 1 [ESTIMATING YIELD CURVE] [BOOTSTRAPPING HISTOGRAM] .............................................................._...................................... [COMPUTING CONFIDENCE INTERVALS] [WRITING OUTPUT]Command completed. Elapsed time: 0:01:42. Running peak memory: 6.567GB. PID: 351439; 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_100/QC_hg38/H9_PRO-seq_100_preseq_counts.txt` > `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_preseq_counts.txt` (351825)
Command completed. Elapsed time: 0:00:25. Running peak memory: 6.567GB. PID: 351825; 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_100/QC_hg38/H9_PRO-seq_100_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_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_100/QC_hg38/H9_PRO-seq_100_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_preseq_plot` (351856)
Processing H9_PRO-seq_100 INFO: Found real counts for H9_PRO-seq_100 - Total (M): 19.4822 Unique (M): 18.471612 Library complexity plot completed!Command completed. Elapsed time: 0:00:04. Running peak memory: 6.567GB. PID: 351856; Command: Rscript; Return code: 0; Memory used: 0.317GB > `Library complexity` QC_hg38/H9_PRO-seq_100_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_100_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_100/QC_hg38/H9_PRO-seq_100_preseq_yield.txt | awk '{print $2}'` > `Frac_exp_unique_at_10M` 0.854 PEPPRO _RES_ ### Calculate NRF, PBC1, and PBC2 (06-15 10:01:53) elapsed: 225.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam` (351899)
Command completed. Elapsed time: 0:00:14. Running peak memory: 6.567GB. PID: 351899; Command: samtools; Return code: 0; Memory used: 0.016GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_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_100/aligned_hg38/H9_PRO-seq_100_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_bamQC.tsv` (351912)
Configured logger 'root' using pararead v0.6 Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam' Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/tmp_H9_PRO-seq_100_PE1_uawr4a94' Processing with 12 cores... Discarding 100 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_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_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', '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_KI270755v1'] Keeping 95 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', 'chr9_KI270720v1_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_KI270466v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270509v1', '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_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']Command completed. Elapsed time: 0:00:15. Running peak memory: 6.567GB. PID: 351912; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.542GB > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_bamQC.tsv` > `NRF` 1.0 PEPPRO _RES_ > `PBC1` 9741100.0 PEPPRO _RES_ > `PBC2` 9741100.0 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_unmap.bam` > `samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_unmap.bam` (351954)
Command completed. Elapsed time: 0:00:08. Running peak memory: 6.567GB. PID: 351954; Command: samtools; Return code: 0; Memory used: 0.009GB > `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_temp.bam` > `Unmapped_reads` 6664276 PEPPRO _RES_ ### Split BAM by strand (06-15 10:02:37) elapsed: 44.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam` > `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam` (352008)
Command completed. Elapsed time: 0:01:03. Running peak memory: 6.567GB. PID: 352008; 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_100/aligned_hg38/H9_PRO-seq_100_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam` (352075)
Command completed. Elapsed time: 0:01:02. Running peak memory: 6.567GB. PID: 352075; Command: samtools; Return code: 0; Memory used: 0.006GB ### Calculate TSS enrichment (06-15 10:04:42) elapsed: 125.0 _TIME_ Missing stat 'TSS_non-coding_score' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/minus_TSS.tsv` > `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (352255)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 352255; Command: sed; Return code: 0; Memory used: 0.002GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_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_100/aligned_hg38/H9_PRO-seq_100_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_plus_TssEnrichment.txt` (352257)
Command completed. Elapsed time: 0:00:06. Running peak memory: 6.567GB. PID: 352257; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.936GB > `TSS_coding_score` 33.8 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_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_100/aligned_hg38/H9_PRO-seq_100_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_minus_TssEnrichment.txt` (352298)
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.567GB. PID: 352298; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.97GB > `TSS_non-coding_score` 12.3 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_TSSenrichment.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R tss -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_minus_TssEnrichment.txt` (352338)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_minus_TssEnrichment.txt `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' TSS enrichment plot completed!Command completed. Elapsed time: 0:00:06. Running peak memory: 6.567GB. PID: 352338; Command: Rscript; Return code: 0; Memory used: 0.317GB > `TSS enrichment` QC_hg38/H9_PRO-seq_100_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_100_TSSenrichment.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt` > `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_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_100/QC_hg38/chr_order.txt` (352368,352369,352370,352371)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 352368; Command: samtools; Return code: 0; Memory used: 0.0GB PID: 352370; Command: awk; Return code: 0; Memory used: 0.0GB PID: 352369; Command: grep; Return code: 0; Memory used: 0.0GB PID: 352371; 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_100/QC_hg38/chr_keep.txt` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_keep.txt` (352373)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 352373; Command: cut; Return code: 0; Memory used: 0.0GB ### Calculate Pause Index (PI) (06-15 10:04:59) elapsed: 17.0 _TIME_ Missing stat 'Pause_index' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_ensembl_gene_body.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_TSS.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_ensembl_tss.bed` (352375,352376)
Command completed. Elapsed time: 0:00:02. Running peak memory: 6.567GB. PID: 352375; Command: grep; Return code: 0; Memory used: 0.002GB PID: 352376; Command: bedtools; Return code: 0; Memory used: 0.051GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/ensembl_gtf/default/hg38_ensembl_gene_body.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_ensembl_gene_body.bed` (352380,352381)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 352380; Command: grep; Return code: 0; Memory used: 0.003GB PID: 352381; 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_100/QC_hg38/H9_PRO-seq_100_TSS_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4,4 -k7,7nr | sort -k4,4 -u > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_TSS_density.bed` (352479,352483,352484,352485)
Command completed. Elapsed time: 0:00:25. Running peak memory: 6.567GB. PID: 352479; Command: bedtools; Return code: 0; Memory used: 0.01GB PID: 352484; Command: sort; Return code: 0; Memory used: 0.014GB PID: 352483; Command: awk; Return code: 0; Memory used: 0.001GB PID: 352485; Command: sort; Return code: 0; Memory used: 0.003GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_gene_body_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_gene_body_density.bed` (352622,352623,352624)
Command completed. Elapsed time: 0:00:28. Running peak memory: 6.567GB. PID: 352623; Command: awk; Return code: 0; Memory used: 0.001GB PID: 352622; Command: bedtools; Return code: 0; Memory used: 0.057GB PID: 352624; Command: sort; Return code: 0; Memory used: 0.009GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_pause_index.bed` > `join --nocheck-order -j4 -o 1.1 1.2 1.3 1.4 1.6 1.7 2.2 2.3 2.7 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_gene_body_density.bed | awk -v OFS=' ' '{ if ($5 == "+"){print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($8-$2)^2))^2), ($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5} else {print $1, $2, $8, $4, sqrt((($6+$9)/sqrt(($3-$7)^2))^2),($6/sqrt(($3-$2)^2))/($9/sqrt(($8-$7)^2)), $5}}' | env LC_COLLATE=C sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/tmpw6dbje6s` (352667,352668,352669)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 352667; Command: join; Return code: 0; Memory used: 0.001GB PID: 352669; Command: env; Return code: 0; Memory used: 0.004GB PID: 352668; 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_100/QC_hg38/tmpw6dbje6s | 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_100/QC_hg38/H9_PRO-seq_100_pause_index.bed` > `awk -v OFS=' ' '{ if ($5 > 0.0187236) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/tmpw6dbje6s > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_pause_index.bed` (352676)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 352676; 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_100/QC_hg38/H9_PRO-seq_100_pause_index.bed | awk ' { a[i++]=$5; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'` > `Pause_index` 34.0 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_pause_index.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R pi --annotate -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_pause_index.bed` (352681)
Pause index plot completed!Command completed. Elapsed time: 0:00:04. Running peak memory: 6.567GB. PID: 352681; Command: Rscript; Return code: 0; Memory used: 0.317GB > `Pause index` QC_hg38/H9_PRO-seq_100_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_100_pause_index.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_pause_index.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_pause_index.bed` (352710)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 352710; Command: pigz; Return code: 0; Memory used: 0.002GB ### Calculate Fraction of Reads in pre-mature mRNA (06-15 10:05:59) elapsed: 60.0 _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_100/aligned_hg38/H9_PRO-seq_100_plus.bam` 18165727.0 7048811 > `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_100/aligned_hg38/H9_PRO-seq_100_minus.bam` 18165727.0 6572286 > `Minus_FRiP` 0.36 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_gene_coverage.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_gene_sort.bed` (353310,353311)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 353310; Command: grep; Return code: 0; Memory used: 0.004GB PID: 353311; 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_100/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_gene_coverage.bed` (353313)
Command completed. Elapsed time: 0:00:27. Running peak memory: 6.567GB. PID: 353313; Command: bedtools; Return code: 0; Memory used: 0.101GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/hg38_annotations.bed` > `ln -sf /project/shefflab/genomes/hg38/feat_annotation/default/hg38_annotations.bed.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/hg38_annotations.bed.gz` (353355)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 353355; 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_100/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/hg38_annotations.bed` (353356)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 353356; Command: pigz; Return code: 0; Memory used: 0.002GB ### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 10:07:02) elapsed: 63.0 _TIME_ > `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/hg38_annotations.bed | sort -u` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Enhancer` > `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/raw/hg38_annotations.bed` (353365)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 353365; 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_100/QC_hg38/Enhancer_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Enhancer_sort.bed` (353367,353368,353369,353370)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 353367; Command: cut; Return code: 0; Memory used: 0.0GB PID: 353368; Command: grep; Return code: 0; Memory used: 0.002GB PID: 353370; Command: bedtools; Return code: 0; Memory used: 0.048GB PID: 353369; 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_100/QC_hg38/H9_PRO-seq_100_Enhancer_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Enhancer_plus_coverage.bed` (353373)
Command completed. Elapsed time: 0:00:12. Running peak memory: 6.567GB. PID: 353373; 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_100/QC_hg38/H9_PRO-seq_100_Enhancer_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Enhancer_minus_coverage.bed` (353385)
Command completed. Elapsed time: 0:00:12. Running peak memory: 6.567GB. PID: 353385; Command: bedtools; Return code: 0; Memory used: 0.01GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_sort.bed` (353397,353398,353399,353400)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 353397; Command: cut; Return code: 0; Memory used: 0.0GB PID: 353398; Command: grep; Return code: 0; Memory used: 0.003GB PID: 353400; Command: bedtools; Return code: 0; Memory used: 0.008GB PID: 353399; 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_100/QC_hg38/H9_PRO-seq_100_Promoter_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_plus_coverage.bed` (353402)
Command completed. Elapsed time: 0:00:12. Running peak memory: 6.567GB. PID: 353402; Command: bedtools; Return code: 0; Memory used: 0.021GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_minus_coverage.bed` (353423)
Command completed. Elapsed time: 0:00:12. Running peak memory: 6.567GB. PID: 353423; Command: bedtools; Return code: 0; Memory used: 0.019GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter Flanking Region` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_Flanking_Region` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_Flanking_Region"` (353444)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 353444; Command: mv; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_Flanking_Region | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed` (353445,353446,353447,353448)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 353445; Command: cut; Return code: 0; Memory used: 0.0GB PID: 353447; Command: cut; Return code: 0; Memory used: 0.001GB PID: 353446; Command: grep; Return code: 0; Memory used: 0.002GB PID: 353448; Command: bedtools; Return code: 0; Memory used: 0.01GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_Flanking_Region_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_Flanking_Region_plus_coverage.bed` (353450)
Command completed. Elapsed time: 0:00:12. Running peak memory: 6.567GB. PID: 353450; 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_100/QC_hg38/H9_PRO-seq_100_Promoter_Flanking_Region_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_Flanking_Region_minus_coverage.bed` (353462)
Command completed. Elapsed time: 0:00:12. Running peak memory: 6.567GB. PID: 353462; Command: bedtools; Return code: 0; Memory used: 0.009GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/5' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/5_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/5_UTR"` (353473)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 353473; Command: mv; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/5_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/5_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/5_UTR_sort.bed` (353474,353475,353476,353477)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 353474; Command: cut; Return code: 0; Memory used: 0.0GB PID: 353475; Command: grep; Return code: 0; Memory used: 0.003GB PID: 353477; Command: bedtools; Return code: 0; Memory used: 0.03GB PID: 353476; 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_100/QC_hg38/H9_PRO-seq_100_5_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_5_UTR_plus_coverage.bed` (353480)
Command completed. Elapsed time: 0:00:12. Running peak memory: 6.567GB. PID: 353480; Command: bedtools; Return code: 0; Memory used: 0.01GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_5_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_5_UTR_minus_coverage.bed` (353492)
Command completed. Elapsed time: 0:00:11. Running peak memory: 6.567GB. PID: 353492; Command: bedtools; Return code: 0; Memory used: 0.011GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/3' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/3_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/3_UTR"` (353512)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 353512; Command: mv; Return code: 0; Memory used: 0.001GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/3_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/3_UTR | cut -f 1-3 | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/3_UTR_sort.bed` (353513,353514,353515,353516)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 353513; Command: cut; Return code: 0; Memory used: 0.0GB PID: 353514; Command: grep; Return code: 0; Memory used: 0.003GB PID: 353516; Command: bedtools; Return code: 0; Memory used: 0.034GB PID: 353515; 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_100/QC_hg38/H9_PRO-seq_100_3_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_3_UTR_plus_coverage.bed` (353519)
Command completed. Elapsed time: 0:00:12. Running peak memory: 6.567GB. PID: 353519; Command: bedtools; Return code: 0; Memory used: 0.011GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_3_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_3_UTR_minus_coverage.bed` (353530)
Command completed. Elapsed time: 0:00:11. Running peak memory: 6.567GB. PID: 353530; Command: bedtools; Return code: 0; Memory used: 0.01GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Exon` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Exon_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Exon_sort.bed` (353541,353542,353543,353544)
Command completed. Elapsed time: 0:00:03. Running peak memory: 6.567GB. PID: 353541; Command: cut; Return code: 0; Memory used: 0.0GB PID: 353542; Command: grep; Return code: 0; Memory used: 0.004GB PID: 353544; Command: bedtools; Return code: 0; Memory used: 0.171GB PID: 353543; 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_100/QC_hg38/H9_PRO-seq_100_Exon_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Exon_plus_coverage.bed` (353549)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.567GB. PID: 353549; 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_100/QC_hg38/H9_PRO-seq_100_Exon_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Exon_minus_coverage.bed` (353596)
Command completed. Elapsed time: 0:00:13. Running peak memory: 6.567GB. PID: 353596; Command: bedtools; Return code: 0; Memory used: 0.014GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Intron` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Intron_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/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_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Intron_sort.bed` (353617,353618,353619,353620)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 353617; Command: cut; Return code: 0; Memory used: 0.0GB PID: 353619; Command: cut; Return code: 0; Memory used: 0.001GB PID: 353618; Command: grep; Return code: 0; Memory used: 0.002GB PID: 353620; 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_100/QC_hg38/H9_PRO-seq_100_Intron_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Intron_plus_coverage.bed` (353623)
Command completed. Elapsed time: 0:00:14. Running peak memory: 6.567GB. PID: 353623; Command: bedtools; Return code: 0; Memory used: 0.087GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Intron_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Intron_minus_coverage.bed` (353638)
Command completed. Elapsed time: 0:00:14. Running peak memory: 6.567GB. PID: 353638; Command: bedtools; Return code: 0; Memory used: 0.027GB ### Plot cFRiF/FRiF (06-15 10:10:02) elapsed: 181.0 _TIME_ > `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_cFRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_100 -z 3099922541 -n 9944138 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Intron_plus_coverage.bed` (353899)
Cumulative cfrif plot completed!Command completed. Elapsed time: 0:00:33. Running peak memory: 6.567GB. PID: 353899; Command: Rscript; Return code: 0; Memory used: 0.505GB > `cFRiF` QC_hg38/H9_PRO-seq_100_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_100_cFRiF.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_FRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_100 -z 3099922541 -n 9944138 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_Intron_plus_coverage.bed` (353943)
Cumulative frif plot completed!Command completed. Elapsed time: 0:00:24. Running peak memory: 6.567GB. PID: 353943; Command: Rscript; Return code: 0; Memory used: 0.507GB > `FRiF` QC_hg38/H9_PRO-seq_100_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_100_FRiF.png PEPPRO _OBJ_ ### Calculate mRNA contamination (06-15 10:11:01) elapsed: 58.0 _TIME_ Missing stat 'mRNA_contamination' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_introns_sort.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_exons.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_exons_sort.bed` (353980,353981)
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.567GB. PID: 353980; Command: grep; Return code: 0; Memory used: 0.004GB PID: 353981; Command: bedtools; Return code: 0; Memory used: 0.101GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_keep.txt /project/shefflab/genomes/hg38/refgene_anno/default/hg38_introns.bed | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_introns_sort.bed` (354045,354046,354047)
Command completed. Elapsed time: 0:00:05. Running peak memory: 6.567GB. PID: 354045; Command: grep; Return code: 0; Memory used: 0.005GB PID: 354047; Command: bedtools; Return code: 0; Memory used: 0.004GB PID: 354046; 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_100/QC_hg38/H9_PRO-seq_100_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_introns_coverage.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_exons_coverage.bed` (354055)
Command completed. Elapsed time: 0:00:24. Running peak memory: 6.567GB. PID: 354055; Command: bedtools; Return code: 0; Memory used: 0.015GB > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_introns_coverage.bed` (354094)
Command completed. Elapsed time: 0:00:27. Running peak memory: 6.567GB. PID: 354094; Command: bedtools; Return code: 0; Memory used: 0.087GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_exons_rpkm.bed` > `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/18.165727)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_exons_rpkm.bed` (354144,354145,354146)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 354144; Command: awk; Return code: 0; Memory used: 0.007GB PID: 354146; Command: sort; Return code: 0; Memory used: 0.003GB PID: 354145; 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_100/QC_hg38/H9_PRO-seq_100_introns_rpkm.bed` > `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/18.165727)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_introns_rpkm.bed` (354149,354150,354151)
Command completed. Elapsed time: 0:00:01. Running peak memory: 6.567GB. PID: 354149; Command: awk; Return code: 0; Memory used: 0.007GB PID: 354151; Command: sort; Return code: 0; Memory used: 0.004GB PID: 354150; 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_100/QC_hg38/H9_PRO-seq_100_exon_intron_ratios.bed` > `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_exons_rpkm.bed | awk -v OFS=' ' 'NF==11 {print $7, $8, $9, $1, ($10/$5), $11}' | sort -k1,1 -k2,2n > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_exon_intron_ratios.bed` (354162,354163,354164)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 354162; Command: join; Return code: 0; Memory used: 0.001GB PID: 354164; Command: sort; Return code: 0; Memory used: 0.004GB PID: 354163; 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_100/QC_hg38/H9_PRO-seq_100_exon_intron_ratios.bed | sort -n | awk ' { a[i++]=$1; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'` > `mRNA_contamination` 1.29 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_mRNA_contamination.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R mrna -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_exon_intron_ratios.bed --annotate` (354171)
mRNA contamination plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 6.567GB. PID: 354171; Command: Rscript; Return code: 0; Memory used: 0.319GB > `mRNA contamination` QC_hg38/H9_PRO-seq_100_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_100_mRNA_contamination.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_exon_intron_ratios.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/QC_hg38/H9_PRO-seq_100_exon_intron_ratios.bed` (354192)
Command completed. Elapsed time: 0:00:00. Running peak memory: 6.567GB. PID: 354192; Command: pigz; Return code: 0; Memory used: 0.005GB ### Produce bigWig files (06-15 10:12:08) elapsed: 67.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_plus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam` (354200)
Command completed. Elapsed time: 0:00:07. Running peak memory: 6.567GB. PID: 354200; Command: samtools; Return code: 0; Memory used: 0.009GB > `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_plus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 18165727.0` (354216)
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_100/aligned_hg38/H9_PRO-seq_100_plus.bam' Temporary files will be stored in: 'tmp_H9_PRO-seq_100_plus_cuttrace_p_mvnz0d' Processing with 4 cores... stdin is empty of data Discarding 112 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_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_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_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_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1'] Keeping 83 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_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_KI270719v1_random', 'chr9_KI270720v1_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_KI270466v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 83 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_plus_exact_body_0-mer.bw' Merging 83 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_plus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:07:07. Running peak memory: 6.567GB. PID: 354216; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.795GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_minus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam` (361551)
Command completed. Elapsed time: 0:00:07. Running peak memory: 6.567GB. PID: 361551; Command: samtools; Return code: 0; Memory used: 0.01GB > `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/aligned_hg38/H9_PRO-seq_100_minus.bam -c /project/shefflab/genomes/hg38/fasta/default/hg38.chrom.sizes -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 18165727.0` (361672)
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_100/aligned_hg38/H9_PRO-seq_100_minus.bam' Temporary files will be stored in: 'tmp_H9_PRO-seq_100_minus_cuttrace_s6_a4ibg' Processing with 4 cores... stdin is empty of data Discarding 111 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_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_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_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_KI270755v1'] Keeping 84 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_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_KI270509v1', 'chrUn_KI270519v1', '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_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 84 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_minus_exact_body_0-mer.bw' Merging 84 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_100/signal_hg38/H9_PRO-seq_100_minus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:07:17. Running peak memory: 6.567GB. PID: 361672; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.634GB ### Pipeline completed. Epilogue * Elapsed time (this run): 3:09:22 * Total elapsed time (all runs): 5:35:42 * Peak memory (this run): 6.5669 GB * Pipeline completed time: 2020-06-15 10:26:47