### Pipeline run code and environment: * Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_40 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 8 -M 10000 --input2 /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R` * Compute host: udc-aw29-20b * Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc * Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/ * Pipeline started at: (06-15 07:17:18) elapsed: 1.0 _TIME_ ### Version log: * Python version: 3.6.6 * Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines` * Pipeline version: 0.9.8 * Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10 * Pipeline branch: * master * Pipeline date: 2020-06-09 11:36:49 -0400 * Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-) ### Arguments passed to pipeline: * `TSS_name`: `None` * `adapter`: `cutadapt` * `anno_name`: `None` * `complexity`: `False` * `config_file`: `peppro.yaml` * `cores`: `8` * `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_40pct_PE1.fastq.gz']` * `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE2.fastq.gz']` * `intron_name`: `None` * `keep`: `False` * `logdev`: `False` * `max_len`: `-1` * `mem`: `10000` * `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_40` * `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_40pct_PE1.fastq.gz Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE2.fastq.gz > `File_mb` 971.29 PEPPRO _RES_ > `Read_type` PAIRED PEPPRO _RES_ > `Genome` hg38 PEPPRO _RES_ Detected PRO input ### Merge/link and fastq conversion: (06-15 07:17:19) elapsed: 1.0 _TIME_ Number of input file sets: 2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R1.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R1.fastq.gz` (12548)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 12548; 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_40/raw/H9_PRO-seq_40_R1.fastq.gz' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R2.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_40pct_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R2.fastq.gz` (12549)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB. PID: 12549; 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_40/raw/H9_PRO-seq_40_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_40/fastq/H9_PRO-seq_40_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2.fastq` > `pigz -f -p 8 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1.fastq` (12550)
Command completed. Elapsed time: 0:00:29. Running peak memory: 0.002GB. PID: 12550; Command: pigz; Return code: 0; Memory used: 0.002GB > `pigz -f -p 8 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2.fastq` (12583)
Command completed. Elapsed time: 0:00:30. Running peak memory: 0.002GB. PID: 12583; Command: pigz; Return code: 0; Memory used: 0.002GB > `Raw_reads` 46292984 PEPPRO _RES_ > `Fastq_reads` 46292984 PEPPRO _RES_ ['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/H9_PRO-seq_40_R2.fastq.gz'] ### FASTQ processing: (06-15 07:18:37) elapsed: 78.0 _TIME_ > `cutadapt --version` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq` > `(cutadapt -j 8 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40_R1_cutadapt.txt` (12654)
Command completed. Elapsed time: 0:00:45. Running peak memory: 1.598GB. PID: 12654; Command: cutadapt; Return code: 0; Memory used: 1.598GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq` (12712,12713)
Command completed. Elapsed time: 0:00:17. Running peak memory: 1.598GB. PID: 12712; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 12713; Command: seqtk; Return code: 0; Memory used: 0.002GB Evaluating read trimming > `Trimmed_reads` 11331720 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_40/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq` (12734)
Started analysis of H9_PRO-seq_40_R1_processed.fastq Approx 5% complete for H9_PRO-seq_40_R1_processed.fastq Approx 10% complete for H9_PRO-seq_40_R1_processed.fastq Approx 15% complete for H9_PRO-seq_40_R1_processed.fastq Approx 20% complete for H9_PRO-seq_40_R1_processed.fastq Approx 25% complete for H9_PRO-seq_40_R1_processed.fastq Approx 30% complete for H9_PRO-seq_40_R1_processed.fastq Approx 35% complete for H9_PRO-seq_40_R1_processed.fastq Approx 40% complete for H9_PRO-seq_40_R1_processed.fastq Approx 45% complete for H9_PRO-seq_40_R1_processed.fastq Approx 50% complete for H9_PRO-seq_40_R1_processed.fastq Approx 55% complete for H9_PRO-seq_40_R1_processed.fastq Approx 60% complete for H9_PRO-seq_40_R1_processed.fastq Approx 65% complete for H9_PRO-seq_40_R1_processed.fastq Approx 70% complete for H9_PRO-seq_40_R1_processed.fastq Approx 75% complete for H9_PRO-seq_40_R1_processed.fastq Approx 80% complete for H9_PRO-seq_40_R1_processed.fastq Approx 85% complete for H9_PRO-seq_40_R1_processed.fastq Approx 90% complete for H9_PRO-seq_40_R1_processed.fastq Approx 95% complete for H9_PRO-seq_40_R1_processed.fastq Analysis complete for H9_PRO-seq_40_R1_processed.fastqCommand completed. Elapsed time: 0:00:30. Running peak memory: 1.598GB. PID: 12734; Command: fastqc; Return code: 0; Memory used: 0.169GB > `FastQC report r1` fastqc/H9_PRO-seq_40_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_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq` > `seqkit rmdup --threads 8 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq` (13017)
[INFO][0m 691509 duplicated records removedCommand completed. Elapsed time: 0:00:19. Running peak memory: 1.598GB. PID: 13017; Command: seqkit; Return code: 0; Memory used: 1.032GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq` (13051,13052)
Command completed. Elapsed time: 0:00:13. Running peak memory: 1.598GB. PID: 13051; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 13052; 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_40/cutadapt/H9_PRO-seq_40_R1_cutadapt.txt | awk '{print $(NF-1)}'` > `Reads_with_adapter` 18342898.0 PEPPRO _RES_ > `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40_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_40/cutadapt/H9_PRO-seq_40_R1_cutadapt.txt` > `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_short.fastq | awk '{print $1}'` > `Uninformative_adapter_reads` 11448553.0 PEPPRO _RES_ > `Duplicate_reads` 691509.0 PEPPRO _RES_ > `Pct_uninformative_adapter_reads` 49.4613 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/processed_R1.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/processed_R1.flag` (13104)
Command completed. Elapsed time: 0:00:00. Running peak memory: 1.598GB. PID: 13104; 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_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq` > `(cutadapt -j 8 -m 10 -O 1 -a GATCGTCGGACTGTAGAACTCTGAAC /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40_R2_cutadapt.txt` (13106)
Command completed. Elapsed time: 0:00:42. Running peak memory: 1.598GB. PID: 13106; Command: cutadapt; Return code: 0; Memory used: 1.093GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq` (13161,13162)
Command completed. Elapsed time: 0:00:14. Running peak memory: 1.598GB. PID: 13161; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 13162; Command: seqtk; Return code: 0; Memory used: 0.002GB Evaluating read trimming > `Trimmed_reads` 22663440 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_40/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq` (13218)
Started analysis of H9_PRO-seq_40_R1_processed.fastq Approx 5% complete for H9_PRO-seq_40_R1_processed.fastq Approx 10% complete for H9_PRO-seq_40_R1_processed.fastq Approx 15% complete for H9_PRO-seq_40_R1_processed.fastq Approx 20% complete for H9_PRO-seq_40_R1_processed.fastq Approx 25% complete for H9_PRO-seq_40_R1_processed.fastq Approx 30% complete for H9_PRO-seq_40_R1_processed.fastq Approx 35% complete for H9_PRO-seq_40_R1_processed.fastq Approx 40% complete for H9_PRO-seq_40_R1_processed.fastq Approx 45% complete for H9_PRO-seq_40_R1_processed.fastq Approx 50% complete for H9_PRO-seq_40_R1_processed.fastq Approx 55% complete for H9_PRO-seq_40_R1_processed.fastq Approx 60% complete for H9_PRO-seq_40_R1_processed.fastq Approx 65% complete for H9_PRO-seq_40_R1_processed.fastq Approx 70% complete for H9_PRO-seq_40_R1_processed.fastq Approx 75% complete for H9_PRO-seq_40_R1_processed.fastq Approx 80% complete for H9_PRO-seq_40_R1_processed.fastq Approx 85% complete for H9_PRO-seq_40_R1_processed.fastq Approx 90% complete for H9_PRO-seq_40_R1_processed.fastq Approx 95% complete for H9_PRO-seq_40_R1_processed.fastq Analysis complete for H9_PRO-seq_40_R1_processed.fastqCommand completed. Elapsed time: 0:00:28. Running peak memory: 1.598GB. PID: 13218; Command: fastqc; Return code: 0; Memory used: 0.169GB > `FastQC report r1` fastqc/H9_PRO-seq_40_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_40/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq` (13257)
Started analysis of H9_PRO-seq_40_R2_trimmed.fastq Approx 5% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 10% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 15% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 20% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 25% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 30% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 35% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 40% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 45% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 50% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 55% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 60% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 65% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 70% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 75% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 80% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 85% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 90% complete for H9_PRO-seq_40_R2_trimmed.fastq Approx 95% complete for H9_PRO-seq_40_R2_trimmed.fastq Analysis complete for H9_PRO-seq_40_R2_trimmed.fastqCommand completed. Elapsed time: 0:00:26. Running peak memory: 1.598GB. PID: 13257; Command: fastqc; Return code: 0; Memory used: 0.164GB > `FastQC report r2` fastqc/H9_PRO-seq_40_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_40/cutadapt/H9_PRO-seq_40.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40.histogram` > `fastq_pair -t 41663685 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq` (13327)
Left paired: 11616977 Right paired: 11616977 Left single: 80962 Right single: 1072452 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq.single.fqCommand completed. Elapsed time: 0:01:12. Running peak memory: 2.274GB. PID: 13327; Command: fastq_pair; Return code: 0; Memory used: 2.274GB > `flash -q -t 8 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_noadap.fastq.paired.fq -o H9_PRO-seq_40 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt` (13389)
Command completed. Elapsed time: 0:00:36. Running peak memory: 2.274GB. PID: 13389; Command: flash; Return code: 0; Memory used: 0.067GB ### Plot adapter insertion distribution (06-15 07:24:55) elapsed: 377.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt/H9_PRO-seq_40_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_40/cutadapt/H9_PRO-seq_40.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/cutadapt -u 8` (13560)
Adapter insertion distribution plot completed!Command completed. Elapsed time: 0:00:08. Running peak memory: 2.274GB. PID: 13560; Command: Rscript; Return code: 0; Memory used: 0.122GB > `Adapter insertion distribution` cutadapt/H9_PRO-seq_40_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_40_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_40/cutadapt/H9_PRO-seq_40.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 07:25:03) elapsed: 8.0 _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_40/cutadapt/H9_PRO-seq_40.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_40/cutadapt/H9_PRO-seq_40.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_40/cutadapt/H9_PRO-seq_40.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_40/cutadapt/H9_PRO-seq_40.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_40/cutadapt/H9_PRO-seq_40.hist` > `Degradation_ratio` 1.0318 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq` > `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq` (13793)
Command completed. Elapsed time: 0:00:05. Running peak memory: 2.274GB. PID: 13793; 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_40/fastq/processed_R2.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/processed_R2.flag` (13800)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.274GB. PID: 13800; 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_40/fastq/repaired.flag` > `fastq_pair -t 41663685 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq` (13801)
Left paired: 11242330 Right paired: 11242330 Left single: 89390 Right single: 1100903 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq.single.fqCommand completed. Elapsed time: 0:01:01. Running peak memory: 2.361GB. PID: 13801; Command: fastq_pair; Return code: 0; Memory used: 2.361GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq` (13855)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.361GB. PID: 13855; Command: mv; Return code: 0; Memory used: 0.002GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq` (13856)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.361GB. PID: 13856; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/repaired.flag` (13857)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.361GB. PID: 13857; 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_40/fastq/dups_repaired.flag` > `fastq_pair -t 41663685 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq` (13858)
Left paired: 10608843 Right paired: 10608843 Left single: 68392 Right single: 1734390 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq.single.fqCommand completed. Elapsed time: 0:00:54. Running peak memory: 2.428GB. PID: 13858; Command: fastq_pair; Return code: 0; Memory used: 2.428GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq` (13906)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB. PID: 13906; Command: mv; Return code: 0; Memory used: 0.001GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq` (13907)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB. PID: 13907; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/dups_repaired.flag` (13909)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB. PID: 13909; Command: touch; Return code: 0; Memory used: 0.0GB ### Prealignments (06-15 07:27:05) elapsed: 122.0 _TIME_ Prealignment assemblies: ['human_rDNA'] ### Map to human_rDNA (06-15 07:27:05) elapsed: 0.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_bt2` (13910)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB. PID: 13910; Command: mkfifo; Return code: 0; Memory used: 0.001GB 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_40/prealignments/H9_PRO-seq_40_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_40/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R2.fq` (13911)
> `(bowtie2 -p 8 -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_40 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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' 11242330 reads; of these: 11242330 (100.00%) were unpaired; of these: 10076783 (89.63%) aligned 0 times 1165547 (10.37%) aligned exactly 1 time 0 (0.00%) aligned >1 times 10.37% overall alignment rate > `Aligned_reads_human_rDNA` 2331094.0 PEPPRO _RES_ > `Alignment_rate_human_rDNA` 10.29 PEPPRO _RES_ ### Map to human_rDNA (06-15 07:28:25) elapsed: 81.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_dups_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_dups_bt2` (13995)
Command completed. Elapsed time: 0:00:00. Running peak memory: 2.428GB. PID: 13995; 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_40/prealignments/H9_PRO-seq_40_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_40/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_dups_R2.fq` (13996)
> `(bowtie2 -p 8 -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_40 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/fastq/H9_PRO-seq_40_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)` not gzipping output 1165547 reads skipped 0 reads lost File not added to cleanup: prealignments/human_rDNA_dups_bt2 ### Map to genome (06-15 07:29:56) elapsed: 90.0 _TIME_ No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_fail_qc_dups.bam Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam` > `bowtie2 -p 8 --very-sensitive -X 2000 --rg-id H9_PRO-seq_40 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_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_40/aligned_hg38/tmpa7932xtf -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam` (14082,14083,14084)
982150 reads skipped 0 reads lost 10076783 reads; of these: 10076783 (100.00%) were paired; of these: 4178107 (41.46%) aligned concordantly 0 times 4837452 (48.01%) aligned concordantly exactly 1 time 1061224 (10.53%) aligned concordantly >1 times ---- 4178107 pairs aligned concordantly 0 times; of these: 929745 (22.25%) aligned discordantly 1 time ---- 3248362 pairs aligned 0 times concordantly or discordantly; of these: 6496724 mates make up the pairs; of these: 2667586 (41.06%) aligned 0 times 1399857 (21.55%) aligned exactly 1 time 2429281 (37.39%) aligned >1 times 86.76% overall alignment rate [bam_sort_core] merging from 5 files and 1 in-memory blocks...Command completed. Elapsed time: 0:25:17. Running peak memory: 3.662GB. PID: 14083; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 14082; Command: bowtie2; Return code: 0; Memory used: 3.662GB PID: 14084; Command: samtools; Return code: 0; Memory used: 0.896GB > `samtools view -q 10 -b -@ 8 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam` (16987)
Command completed. Elapsed time: 0:00:39. Running peak memory: 3.662GB. PID: 16987; Command: samtools; Return code: 0; Memory used: 0.015GB > `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_40/aligned_hg38/H9_PRO-seq_40_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'` > `Mapped_reads` 17485980 PEPPRO _RES_ > `QC_filtered_reads` 10220292 PEPPRO _RES_ > `Aligned_reads` 7265688.5 PEPPRO _RES_ > `Alignment_rate` 32.06 PEPPRO _RES_ > `Total_efficiency` 15.7 PEPPRO _RES_ > `Read_depth` 2.14 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam` > `bowtie2 -p 8 --very-sensitive -X 2000 --rg-id H9_PRO-seq_40 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_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_40/aligned_hg38/tmpa7932xtf -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp_dups.bam` (17690,17695,17696)
9626693 reads; of these: 9626693 (100.00%) were paired; of these: 3912255 (40.64%) aligned concordantly 0 times 4695529 (48.78%) aligned concordantly exactly 1 time 1018909 (10.58%) aligned concordantly >1 times ---- 3912255 pairs aligned concordantly 0 times; of these: 903759 (23.10%) aligned discordantly 1 time ---- 3008496 pairs aligned 0 times concordantly or discordantly; of these: 6016992 mates make up the pairs; of these: 2491165 (41.40%) aligned 0 times 1357608 (22.56%) aligned exactly 1 time 2168219 (36.03%) aligned >1 times 87.06% overall alignment rate [bam_sort_core] merging from 5 files and 1 in-memory blocks...Command completed. Elapsed time: 0:23:59. Running peak memory: 3.662GB. PID: 17690; Command: bowtie2; Return code: 0; Memory used: 3.65GB PID: 17695; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 17696; Command: samtools; Return code: 0; Memory used: 0.896GB > `samtools view -q 10 -b -@ 8 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam` (20007)
Command completed. Elapsed time: 0:00:37. Running peak memory: 3.662GB. PID: 20007; Command: samtools; Return code: 0; Memory used: 0.015GB ### Compress all unmapped read files (06-15 08:27:43) elapsed: 3468.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R1.fq.gz` > `pigz -f -p 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R1.fq` (20054)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.662GB. PID: 20054; Command: pigz; Return code: 0; Memory used: 0.006GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R2.fq.gz` > `pigz -f -p 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/prealignments/H9_PRO-seq_40_human_rDNA_unmap_R2.fq` (20078)
Command completed. Elapsed time: 0:00:13. Running peak memory: 3.662GB. PID: 20078; Command: pigz; Return code: 0; Memory used: 0.006GB Missing stat 'Mitochondrial_reads' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam` (20099)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.662GB. PID: 20099; Command: samtools; Return code: 0; Memory used: 0.018GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3` > `Mitochondrial_reads` 336077 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_noMT.bam` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam` (20117)
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.662GB. PID: 20117; Command: samtools; Return code: 0; Memory used: 0.008GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/aligned_hg38/chr_sizes.bed` (20127,20128,20129,20130)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 20128; Command: cut; Return code: 0; Memory used: 0.0GB PID: 20130; Command: grep; Return code: 0; Memory used: 0.0GB PID: 20127; Command: samtools; Return code: 0; Memory used: 0.01GB PID: 20129; Command: awk; Return code: 0; Memory used: 0.0GB > `samtools view -L /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/chr_sizes.bed -b -@ 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_noMT.bam` (20132)
Command completed. Elapsed time: 0:00:17. Running peak memory: 3.662GB. PID: 20132; Command: samtools; Return code: 0; Memory used: 0.016GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam` (20158)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 20158; Command: mv; Return code: 0; Memory used: 0.001GB > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam` (20159)
Command completed. Elapsed time: 0:00:11. Running peak memory: 3.662GB. PID: 20159; Command: samtools; Return code: 0; Memory used: 0.008GB ### Split BAM file (06-15 08:29:06) elapsed: 83.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam | samtools sort - -@ 8 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam` (20169,20170)
[bam_sort_core] merging from 0 files and 8 in-memory blocks...Command completed. Elapsed time: 0:01:06. Running peak memory: 3.662GB. PID: 20169; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 20170; Command: samtools; Return code: 0; Memory used: 2.08GB > `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort.bam | samtools sort - -@ 8 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE2.bam` (20511,20512)
[bam_sort_core] merging from 0 files and 8 in-memory blocks...Command completed. Elapsed time: 0:00:55. Running peak memory: 3.662GB. PID: 20511; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 20512; Command: samtools; Return code: 0; Memory used: 1.665GB Missing stat 'Maximum_read_length' > `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_temp_dups.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp_dups.bam` (20612)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.662GB. PID: 20612; Command: samtools; Return code: 0; Memory used: 0.019GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam` No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam.bai Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam | samtools sort - -@ 8 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam` (20630,20631)
[bam_sort_core] merging from 0 files and 8 in-memory blocks...Command completed. Elapsed time: 0:01:05. Running peak memory: 3.662GB. PID: 20630; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 20631; Command: samtools; Return code: 0; Memory used: 2.058GB > `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_sort_dups.bam | samtools sort - -@ 8 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE2.bam` (20711,20712)
[bam_sort_core] merging from 0 files and 8 in-memory blocks...Command completed. Elapsed time: 0:00:55. Running peak memory: 3.662GB. PID: 20711; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 20712; Command: samtools; Return code: 0; Memory used: 1.648GB ### Calculate library complexity (06-15 08:33:47) elapsed: 281.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_out.txt` > `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam` (20786)
BAM_INPUT TOTAL READS = 7703559 COUNTS_SUM = 7703559 DISTINCT READS = 6.71206e+06 DISTINCT COUNTS = 185 MAX COUNT = 13085 COUNTS OF 1 = 6.20795e+06 OBSERVED COUNTS (13086) 1 6207952 2 358767 3 75714 4 28508 5 14029 6 7631 7 4735 8 3035 9 2128 10 1643 11 1174 12 916 13 690 14 602 15 507 16 401 17 353 18 333 19 270 20 213 21 177 22 163 23 157 24 134 25 146 26 121 27 103 28 88 29 88 30 64 31 55 32 80 33 58 34 53 35 43 36 36 37 46 38 47 39 39 40 41 41 33 42 34 43 27 44 21 45 15 46 24 47 31 48 24 49 22 50 12 51 21 52 16 53 25 54 9 55 14 56 10 57 16 58 16 59 15 60 10 61 7 62 10 63 9 64 10 65 7 66 8 67 4 68 12 69 11 70 8 71 5 72 4 73 4 74 5 75 5 76 3 77 5 78 4 79 3 80 7 81 5 82 4 83 6 84 5 85 3 86 5 87 3 88 10 89 3 90 4 91 7 92 2 93 6 95 2 96 5 97 4 99 2 100 1 101 1 102 2 103 3 104 1 105 4 106 2 107 3 109 1 110 2 111 3 112 1 113 1 114 2 118 1 120 2 121 2 122 1 123 1 124 1 125 3 126 3 128 3 129 2 130 1 132 2 133 2 135 1 137 1 139 2 140 3 141 2 143 1 145 1 148 2 150 1 151 1 152 2 154 1 155 1 158 1 161 1 163 1 165 1 170 2 171 1 174 1 188 1 190 1 201 1 206 1 209 1 211 2 215 1 219 2 221 1 222 1 223 1 231 1 242 1 275 1 283 1 284 1 287 1 288 2 289 1 374 1 375 1 377 1 448 1 473 1 491 1 545 1 572 1 677 1 827 1 831 1 833 1 1005 1 1061 1 1083 1 1493 1 1906 1 3867 1 4608 1 5719 1 12251 1 13085 1 sample size: 1000000 sample size: 2000000 sample size: 3000000 sample size: 4000000 sample size: 5000000 sample size: 6000000 sample size: 7000000Command completed. Elapsed time: 0:00:42. Running peak memory: 3.662GB. PID: 20786; 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_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt` > `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam` (20822)
BAM_INPUT TOTAL READS = 7703559 DISTINCT READS = 6.71206e+06 DISTINCT COUNTS = 185 MAX COUNT = 13085 COUNTS OF 1 = 6.20795e+06 MAX TERMS = 92 OBSERVED COUNTS (13086) 1 6207952 2 358767 3 75714 4 28508 5 14029 6 7631 7 4735 8 3035 9 2128 10 1643 11 1174 12 916 13 690 14 602 15 507 16 401 17 353 18 333 19 270 20 213 21 177 22 163 23 157 24 134 25 146 26 121 27 103 28 88 29 88 30 64 31 55 32 80 33 58 34 53 35 43 36 36 37 46 38 47 39 39 40 41 41 33 42 34 43 27 44 21 45 15 46 24 47 31 48 24 49 22 50 12 51 21 52 16 53 25 54 9 55 14 56 10 57 16 58 16 59 15 60 10 61 7 62 10 63 9 64 10 65 7 66 8 67 4 68 12 69 11 70 8 71 5 72 4 73 4 74 5 75 5 76 3 77 5 78 4 79 3 80 7 81 5 82 4 83 6 84 5 85 3 86 5 87 3 88 10 89 3 90 4 91 7 92 2 93 6 95 2 96 5 97 4 99 2 100 1 101 1 102 2 103 3 104 1 105 4 106 2 107 3 109 1 110 2 111 3 112 1 113 1 114 2 118 1 120 2 121 2 122 1 123 1 124 1 125 3 126 3 128 3 129 2 130 1 132 2 133 2 135 1 137 1 139 2 140 3 141 2 143 1 145 1 148 2 150 1 151 1 152 2 154 1 155 1 158 1 161 1 163 1 165 1 170 2 171 1 174 1 188 1 190 1 201 1 206 1 209 1 211 2 215 1 219 2 221 1 222 1 223 1 231 1 242 1 275 1 283 1 284 1 287 1 288 2 289 1 374 1 375 1 377 1 448 1 473 1 491 1 545 1 572 1 677 1 827 1 831 1 833 1 1005 1 1061 1 1083 1 1493 1 1906 1 3867 1 4608 1 5719 1 12251 1 13085 1 [ESTIMATING YIELD CURVE] [BOOTSTRAPPING HISTOGRAM] ..............._.................................._................................................... [COMPUTING CONFIDENCE INTERVALS] [WRITING OUTPUT]Command completed. Elapsed time: 0:00:46. Running peak memory: 3.662GB. PID: 20822; Command: preseq; Return code: 0; Memory used: 0.011GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_counts.txt` > `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_counts.txt` (21058)
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.662GB. PID: 21058; 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_40/QC_hg38/H9_PRO-seq_40_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_preseq_plot` (21073)
Processing H9_PRO-seq_40 INFO: Found real counts for H9_PRO-seq_40 - Total (M): 7.79292 Unique (M): 7.703559 Library complexity plot completed!Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21073; Command: Rscript; Return code: 0; Memory used: 0.204GB > `Library complexity` QC_hg38/H9_PRO-seq_40_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_preseq_yield.txt | awk '{print $2}'` > `Frac_exp_unique_at_10M` 0.8539 PEPPRO _RES_ ### Calculate NRF, PBC1, and PBC2 (06-15 08:35:33) elapsed: 106.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam` (21093)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21093; Command: samtools; Return code: 0; Memory used: 0.011GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -c 8 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_bamQC.tsv` (21104)
Configured logger 'root' using pararead v0.6 Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam' Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/tmp_H9_PRO-seq_40_PE1_n6fxgr9j' Processing with 8 cores... Discarding 106 chunk(s) of reads: ['chrM', 'chr1_KI270708v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270745v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1'] Keeping 89 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_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']Command completed. Elapsed time: 0:00:11. Running peak memory: 3.662GB. PID: 21104; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 0.84GB > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_bamQC.tsv` > `NRF` 1.0 PEPPRO _RES_ > `PBC1` 3896460.0 PEPPRO _RES_ > `PBC2` 3896460.0 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_unmap.bam` > `samtools view -b -@ 8 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_unmap.bam` (21161)
Command completed. Elapsed time: 0:00:04. Running peak memory: 3.662GB. PID: 21161; Command: samtools; Return code: 0; Memory used: 0.013GB > `samtools view -c -f 4 -@ 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_temp.bam` > `Unmapped_reads` 2667586 PEPPRO _RES_ ### Split BAM by strand (06-15 08:35:58) elapsed: 24.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam` > `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam` (21190)
Command completed. Elapsed time: 0:00:29. Running peak memory: 3.662GB. PID: 21190; 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_40/aligned_hg38/H9_PRO-seq_40_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam` (21215)
Command completed. Elapsed time: 0:00:28. Running peak memory: 3.662GB. PID: 21215; Command: samtools; Return code: 0; Memory used: 0.006GB ### Calculate TSS enrichment (06-15 08:36:55) elapsed: 57.0 _TIME_ Missing stat 'TSS_non-coding_score' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/minus_TSS.tsv` > `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (21242)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21242; 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_40/QC_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/plus_TSS.tsv -p ends -c 8 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_plus_TssEnrichment.txt` (21243)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB. PID: 21243; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.567GB > `TSS_coding_score` 33.6 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/minus_TSS.tsv -p ends -c 8 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_minus_TssEnrichment.txt` (21266)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB. PID: 21266; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.695GB > `TSS_non-coding_score` 12.3 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_minus_TssEnrichment.txt` (21288)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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: 0:00:07. Running peak memory: 3.662GB. PID: 21288; Command: Rscript; Return code: 0; Memory used: 0.316GB > `TSS enrichment` QC_hg38/H9_PRO-seq_40_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_40_TSSenrichment.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt` > `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/QC_hg38/chr_order.txt` (21309,21310,21311,21312)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21309; Command: samtools; Return code: 0; Memory used: 0.0GB PID: 21311; Command: awk; Return code: 0; Memory used: 0.0GB PID: 21310; Command: grep; Return code: 0; Memory used: 0.0GB PID: 21312; 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_40/QC_hg38/chr_keep.txt` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_keep.txt` (21314)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21314; Command: cut; Return code: 0; Memory used: 0.0GB ### Calculate Pause Index (PI) (06-15 08:37:12) elapsed: 17.0 _TIME_ Missing stat 'Pause_index' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_gene_body.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_tss.bed` (21316,21317)
Command completed. Elapsed time: 0:00:02. Running peak memory: 3.662GB. PID: 21316; Command: grep; Return code: 0; Memory used: 0.004GB PID: 21317; Command: bedtools; Return code: 0; Memory used: 0.093GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_gene_body.bed` (21321,21322)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21321; Command: grep; Return code: 0; Memory used: 0.003GB PID: 21322; Command: bedtools; Return code: 0; Memory used: 0.022GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_TSS_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/H9_PRO-seq_40_TSS_density.bed` (21324,21325,21326,21327)
Command completed. Elapsed time: 0:00:12. Running peak memory: 3.662GB. PID: 21326; Command: sort; Return code: 0; Memory used: 0.008GB PID: 21324; Command: bedtools; Return code: 0; Memory used: 0.007GB PID: 21327; Command: sort; Return code: 0; Memory used: 0.003GB PID: 21325; 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_40/QC_hg38/H9_PRO-seq_40_gene_body_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_gene_body_density.bed` (21339,21340,21341)
Command completed. Elapsed time: 0:00:16. Running peak memory: 3.662GB. PID: 21339; Command: bedtools; Return code: 0; Memory used: 0.055GB PID: 21341; Command: sort; Return code: 0; Memory used: 0.005GB PID: 21340; 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_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/tmp2cnv4nn_` (21356,21357,21358)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21356; Command: join; Return code: 0; Memory used: 0.001GB PID: 21358; Command: env; Return code: 0; Memory used: 0.004GB PID: 21357; 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_40/QC_hg38/tmp2cnv4nn_ | 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_40/QC_hg38/H9_PRO-seq_40_pause_index.bed` > `awk -v OFS=' ' '{ if ($5 > 0.0086562) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/tmp2cnv4nn_ > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_pause_index.bed` (21364)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21364; 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_40/QC_hg38/H9_PRO-seq_40_pause_index.bed | awk ' { a[i++]=$5; } END { x=int((i+1)/2); if (x < (i+1)/2) print (a[x-1]+a[x])/2; else print a[x-1]; }'` > `Pause_index` 33.24 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_pause_index.bed` (21369)
Pause index plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB. PID: 21369; Command: Rscript; Return code: 0; Memory used: 0.296GB > `Pause index` QC_hg38/H9_PRO-seq_40_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_40_pause_index.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_pause_index.bed.gz` > `pigz -f -p 8 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_pause_index.bed` (21388)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21388; Command: pigz; Return code: 0; Memory used: 0.002GB ### Calculate Fraction of Reads in pre-mature mRNA (06-15 08:37:48) elapsed: 36.0 _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_40/aligned_hg38/H9_PRO-seq_40_plus.bam` 7265688.5 2820700 > `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_40/aligned_hg38/H9_PRO-seq_40_minus.bam` 7265688.5 2629275 > `Minus_FRiP` 0.36 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_gene_coverage.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_gene_sort.bed` (21418,21419)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB. PID: 21418; Command: grep; Return code: 0; Memory used: 0.004GB PID: 21419; 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_40/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_gene_coverage.bed` (21422)
Command completed. Elapsed time: 0:00:15. Running peak memory: 3.662GB. PID: 21422; Command: bedtools; Return code: 0; Memory used: 0.055GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/raw/hg38_annotations.bed.gz` (21437)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21437; Command: ln; Return code: 0; Memory used: 0.0GB > `pigz -f -p 8 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/hg38_annotations.bed` (21438)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21438; Command: pigz; Return code: 0; Memory used: 0.002GB ### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 08:38:19) elapsed: 31.0 _TIME_ > `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/hg38_annotations.bed | sort -u` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Enhancer` > `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/raw/hg38_annotations.bed` (21446)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB. PID: 21446; 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_40/QC_hg38/Enhancer_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Enhancer_sort.bed` (21449,21450,21451,21452)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB. PID: 21449; Command: cut; Return code: 0; Memory used: 0.0GB PID: 21450; Command: grep; Return code: 0; Memory used: 0.002GB PID: 21452; Command: bedtools; Return code: 0; Memory used: 0.044GB PID: 21451; 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_40/QC_hg38/H9_PRO-seq_40_Enhancer_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Enhancer_plus_coverage.bed` (21454)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21454; 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_40/QC_hg38/H9_PRO-seq_40_Enhancer_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Enhancer_minus_coverage.bed` (21461)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB. PID: 21461; Command: bedtools; Return code: 0; Memory used: 0.008GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_sort.bed` (21467,21468,21469,21470)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21467; Command: cut; Return code: 0; Memory used: 0.0GB PID: 21468; Command: grep; Return code: 0; Memory used: 0.003GB PID: 21470; Command: bedtools; Return code: 0; Memory used: 0.008GB PID: 21469; 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_40/QC_hg38/H9_PRO-seq_40_Promoter_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_plus_coverage.bed` (21472)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21472; 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_40/QC_hg38/H9_PRO-seq_40_Promoter_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_minus_coverage.bed` (21479)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21479; Command: bedtools; Return code: 0; Memory used: 0.012GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter Flanking Region` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region"` (21485)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21485; Command: mv; Return code: 0; Memory used: 0.0GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region_sort.bed` (21486,21487,21488,21489)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB. PID: 21486; Command: cut; Return code: 0; Memory used: 0.0GB PID: 21488; Command: cut; Return code: 0; Memory used: 0.001GB PID: 21487; Command: grep; Return code: 0; Memory used: 0.002GB PID: 21489; Command: bedtools; Return code: 0; Memory used: 0.048GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_plus_coverage.bed` (21492)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21492; 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_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_minus_coverage.bed` (21499)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21499; Command: bedtools; Return code: 0; Memory used: 0.012GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR"` (21505)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21505; Command: mv; Return code: 0; Memory used: 0.002GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR_sort.bed` (21507,21508,21509,21510)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB. PID: 21507; Command: cut; Return code: 0; Memory used: 0.0GB PID: 21508; Command: grep; Return code: 0; Memory used: 0.003GB PID: 21510; Command: bedtools; Return code: 0; Memory used: 0.01GB PID: 21509; 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_40/QC_hg38/H9_PRO-seq_40_5_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_5_UTR_plus_coverage.bed` (21512)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21512; 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_40/QC_hg38/H9_PRO-seq_40_5_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_5_UTR_minus_coverage.bed` (21519)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB. PID: 21519; Command: bedtools; Return code: 0; Memory used: 0.008GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR"` (21525)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21525; 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_40/QC_hg38/3_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR_sort.bed` (21526,21527,21528,21529)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB. PID: 21526; Command: cut; Return code: 0; Memory used: 0.0GB PID: 21527; Command: grep; Return code: 0; Memory used: 0.003GB PID: 21529; Command: bedtools; Return code: 0; Memory used: 0.01GB PID: 21528; 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_40/QC_hg38/H9_PRO-seq_40_3_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_3_UTR_plus_coverage.bed` (21531)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21531; 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_40/QC_hg38/H9_PRO-seq_40_3_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_3_UTR_minus_coverage.bed` (21539)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB. PID: 21539; Command: bedtools; Return code: 0; Memory used: 0.008GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon_sort.bed` (21546,21547,21548,21549)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.662GB. PID: 21546; Command: cut; Return code: 0; Memory used: 0.0GB PID: 21547; Command: grep; Return code: 0; Memory used: 0.003GB PID: 21549; Command: bedtools; Return code: 0; Memory used: 0.158GB PID: 21548; 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_40/QC_hg38/H9_PRO-seq_40_Exon_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_plus_coverage.bed` (21554)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.662GB. PID: 21554; Command: bedtools; Return code: 0; Memory used: 0.016GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_minus_coverage.bed` (21561)
Command completed. Elapsed time: 0:00:07. Running peak memory: 3.662GB. PID: 21561; Command: bedtools; Return code: 0; Memory used: 0.012GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron_sort.bed` (21568,21569,21570,21571)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB. PID: 21568; Command: cut; Return code: 0; Memory used: 0.0GB PID: 21570; Command: cut; Return code: 0; Memory used: 0.001GB PID: 21569; Command: grep; Return code: 0; Memory used: 0.002GB PID: 21571; Command: bedtools; Return code: 0; Memory used: 0.077GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_plus_coverage.bed` (21574)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.662GB. PID: 21574; Command: bedtools; Return code: 0; Memory used: 0.041GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_minus_coverage.bed` (21583)
Command completed. Elapsed time: 0:00:08. Running peak memory: 3.662GB. PID: 21583; Command: bedtools; Return code: 0; Memory used: 0.022GB ### Plot cFRiF/FRiF (06-15 08:39:54) elapsed: 95.0 _TIME_ > `samtools view -@ 8 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_cFRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_40 -z 3099922541 -n 3978050 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_plus_coverage.bed` (21601)
Cumulative cfrif plot completed!Command completed. Elapsed time: 0:00:38. Running peak memory: 3.662GB. PID: 21601; Command: Rscript; Return code: 0; Memory used: 0.438GB > `cFRiF` QC_hg38/H9_PRO-seq_40_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_40_cFRiF.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_FRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_40 -z 3099922541 -n 3978050 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_Intron_plus_coverage.bed` (21892)
Cumulative frif plot completed!Command completed. Elapsed time: 0:00:29. Running peak memory: 3.662GB. PID: 21892; Command: Rscript; Return code: 0; Memory used: 0.438GB > `FRiF` QC_hg38/H9_PRO-seq_40_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_40_FRiF.png PEPPRO _OBJ_ ### Calculate mRNA contamination (06-15 08:41:01) elapsed: 67.0 _TIME_ Missing stat 'mRNA_contamination' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_introns_sort.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_exons_sort.bed` (21927,21928)
Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB. PID: 21928; Command: bedtools; Return code: 0; Memory used: 0.086GB PID: 21927; Command: grep; Return code: 0; Memory used: 0.004GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/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_40/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_introns_sort.bed` (21934,21935,21936)
Command completed. Elapsed time: 0:00:06. Running peak memory: 3.662GB. PID: 21934; Command: grep; Return code: 0; Memory used: 0.005GB PID: 21936; Command: bedtools; Return code: 0; Memory used: 0.003GB PID: 21935; Command: bedtools; Return code: 0; Memory used: 0.033GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_coverage.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exons_coverage.bed` (21942)
Command completed. Elapsed time: 0:00:11. Running peak memory: 3.662GB. PID: 21942; Command: bedtools; Return code: 0; Memory used: 0.008GB > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_coverage.bed` (21953)
Command completed. Elapsed time: 0:00:13. Running peak memory: 3.662GB. PID: 21953; Command: bedtools; Return code: 0; Memory used: 0.019GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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]/7.2656885)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exons_rpkm.bed` (21965,21966,21967)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB. PID: 21965; Command: awk; Return code: 0; Memory used: 0.007GB PID: 21967; Command: sort; Return code: 0; Memory used: 0.004GB PID: 21966; 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_40/QC_hg38/H9_PRO-seq_40_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]/7.2656885)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_rpkm.bed` (21970,21971,21972)
Command completed. Elapsed time: 0:00:01. Running peak memory: 3.662GB. PID: 21970; Command: awk; Return code: 0; Memory used: 0.007GB PID: 21972; Command: sort; Return code: 0; Memory used: 0.004GB PID: 21971; 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_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed` > `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed` (21974,21975,21976)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 21974; Command: join; Return code: 0; Memory used: 0.001GB PID: 21976; Command: sort; Return code: 0; Memory used: 0.004GB PID: 21975; 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_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_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_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed --annotate` (21983)
mRNA contamination plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 3.662GB. PID: 21983; Command: Rscript; Return code: 0; Memory used: 0.295GB > `mRNA contamination` QC_hg38/H9_PRO-seq_40_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_40_mRNA_contamination.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed.gz` > `pigz -f -p 8 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/QC_hg38/H9_PRO-seq_40_exon_intron_ratios.bed` (22003)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.662GB. PID: 22003; Command: pigz; Return code: 0; Memory used: 0.002GB ### Produce bigWig files (06-15 08:41:43) elapsed: 42.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_plus.bam` (22011)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.662GB. PID: 22011; Command: samtools; Return code: 0; Memory used: 0.006GB > `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/signal_hg38/H9_PRO-seq_40_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_smooth_body_0-mer.bw -p 5 --variable-step --tail-edge --scale 7265688.5` (22015)
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_40/aligned_hg38/H9_PRO-seq_40_plus.bam' Temporary files will be stored in: 'tmp_H9_PRO-seq_40_plus_cuttrace_yc274ool' Processing with 2 cores... stdin is empty of data Discarding 124 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270710v1_random', 'chr1_KI270714v1_random', 'chr2_KI270715v1_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270720v1_random', 'chr14_GL000009v2_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1'] Keeping 71 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr9_KI270719v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 71 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_exact_body_0-mer.bw' Merging 71 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_plus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:09:57. Running peak memory: 3.662GB. PID: 22015; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.633GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_minus.bam` (23614)
Command completed. Elapsed time: 0:00:03. Running peak memory: 3.662GB. PID: 23614; Command: samtools; Return code: 0; Memory used: 0.005GB > `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/aligned_hg38/H9_PRO-seq_40_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_40/signal_hg38/H9_PRO-seq_40_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_smooth_body_0-mer.bw -p 5 --variable-step --tail-edge --scale 7265688.5` (23618)
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_40/aligned_hg38/H9_PRO-seq_40_minus.bam' Temporary files will be stored in: 'tmp_H9_PRO-seq_40_minus_cuttrace_hhgm_zea' Processing with 2 cores... stdin is empty of data Discarding 123 chunk(s) of reads: ['chrM', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_KI270722v1_random', 'chr14_KI270723v1_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270745v1', 'chrUn_KI270748v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_GL000214v1'] Keeping 72 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr14_GL000225v1_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_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 72 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_exact_body_0-mer.bw' Merging 72 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_40/signal_hg38/H9_PRO-seq_40_minus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:09:51. Running peak memory: 3.662GB. PID: 23618; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.634GB ### Pipeline completed. Epilogue * Elapsed time (this run): 1:44:21 * Total elapsed time (all runs): 3:08:26 * Peak memory (this run): 3.6624 GB * Pipeline completed time: 2020-06-15 09:01:38