### Pipeline run code and environment: * Command: `/scratch/jps3dp/tools/databio//peppro/pipelines/peppro.py --sample-name H9_PRO-seq_80 --genome hg38 --input /project/shefflab/data//guertin/fastq/H9_PRO-seq_80pct_PE1.fastq.gz --single-or-paired PAIRED -O /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline -P 12 -M 12000 --input2 /project/shefflab/data//guertin/fastq/H9_PRO-seq_80pct_PE2.fastq.gz --protocol PRO --umi-len 8 --scale --prealignments human_rDNA --dirty -R` * Compute host: udc-ba26-35c0 * Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc * Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/ * Pipeline started at: (06-15 07:17:27) elapsed: 2.0 _TIME_ ### Version log: * Python version: 3.6.6 * Pypiper dir: `/sfs/qumulo/qhome/jps3dp/.local/lib/python3.6/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/peppro/pipelines` * Pipeline version: 0.9.8 * Pipeline hash: 887a9a85408962dc3ca070dc954e59a5d4d73a10 * Pipeline branch: * master * Pipeline date: 2020-06-09 11:36:49 -0400 * Pipeline diff: 40 files changed, 16413 insertions(+), 3702 deletions(-) ### Arguments passed to pipeline: * `TSS_name`: `None` * `adapter`: `cutadapt` * `anno_name`: `None` * `complexity`: `False` * `config_file`: `peppro.yaml` * `cores`: `12` * `coverage`: `False` * `dedup`: `seqkit` * `dirty`: `True` * `ensembl_gene_body`: `None` * `ensembl_tss`: `None` * `exon_name`: `None` * `force_follow`: `False` * `genome_assembly`: `hg38` * `input`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_80pct_PE1.fastq.gz']` * `input2`: `['/project/shefflab/data//guertin/fastq/H9_PRO-seq_80pct_PE2.fastq.gz']` * `intron_name`: `None` * `keep`: `False` * `logdev`: `False` * `max_len`: `-1` * `mem`: `12000` * `new_start`: `False` * `no_fifo`: `False` * `output_parent`: `/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline` * `paired_end`: `True` * `pre_name`: `None` * `prealignments`: `['human_rDNA']` * `prioritize`: `False` * `protocol`: `PRO` * `recover`: `True` * `sample_name`: `H9_PRO-seq_80` * `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_80pct_PE1.fastq.gz Local input file: /project/shefflab/data//guertin/fastq/H9_PRO-seq_80pct_PE2.fastq.gz > `File_mb` 1912.05 PEPPRO _RES_ > `Read_type` PAIRED PEPPRO _RES_ > `Genome` hg38 PEPPRO _RES_ Detected PRO input ### Merge/link and fastq conversion: (06-15 07:17:28) elapsed: 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_80/raw/H9_PRO-seq_80_R1.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_80pct_PE1.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/H9_PRO-seq_80_R1.fastq.gz` (217613)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0GB. PID: 217613; 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_80/raw/H9_PRO-seq_80_R1.fastq.gz' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/H9_PRO-seq_80_R2.fastq.gz` > `ln -sf /project/shefflab/data//guertin/fastq/H9_PRO-seq_80pct_PE2.fastq.gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/H9_PRO-seq_80_R2.fastq.gz` (217615)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB. PID: 217615; 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_80/raw/H9_PRO-seq_80_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_80/fastq/H9_PRO-seq_80_R1.fastq`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2.fastq` > `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/H9_PRO-seq_80_R1.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1.fastq` (217618)
Command completed. Elapsed time: 0:02:50. Running peak memory: 0.002GB. PID: 217618; Command: pigz; Return code: 0; Memory used: 0.002GB > `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/H9_PRO-seq_80_R2.fastq.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2.fastq` (350866)
Command completed. Elapsed time: 0:02:20. Running peak memory: 0.002GB. PID: 350866; Command: pigz; Return code: 0; Memory used: 0.002GB > `Raw_reads` 92574794 PEPPRO _RES_ > `Fastq_reads` 92574794 PEPPRO _RES_ ['/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/H9_PRO-seq_80_R1.fastq.gz', '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/H9_PRO-seq_80_R2.fastq.gz'] ### FASTQ processing: (06-15 07:25:03) elapsed: 455.0 _TIME_ > `cutadapt --version` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq` > `(cutadapt -j 12 -m 10 -O 1 -a TGGAATTCTCGGGTGCCAAGG /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/cutadapt/H9_PRO-seq_80_R1_cutadapt.txt` (171390)
Command completed. Elapsed time: 0:02:03. Running peak memory: 3.293GB. PID: 171390; Command: cutadapt; Return code: 0; Memory used: 3.293GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq` (332651,332652)
Command completed. Elapsed time: 0:01:15. Running peak memory: 3.293GB. PID: 332652; Command: seqtk; Return code: 0; Memory used: 0.002GB PID: 332651; Command: seqtk; Return code: 0; Memory used: 0.001GB Evaluating read trimming > `Trimmed_reads` 22665363 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_80/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq` (332727)
Started analysis of H9_PRO-seq_80_R1_processed.fastq Approx 5% complete for H9_PRO-seq_80_R1_processed.fastq Approx 10% complete for H9_PRO-seq_80_R1_processed.fastq Approx 15% complete for H9_PRO-seq_80_R1_processed.fastq Approx 20% complete for H9_PRO-seq_80_R1_processed.fastq Approx 25% complete for H9_PRO-seq_80_R1_processed.fastq Approx 30% complete for H9_PRO-seq_80_R1_processed.fastq Approx 35% complete for H9_PRO-seq_80_R1_processed.fastq Approx 40% complete for H9_PRO-seq_80_R1_processed.fastq Approx 45% complete for H9_PRO-seq_80_R1_processed.fastq Approx 50% complete for H9_PRO-seq_80_R1_processed.fastq Approx 55% complete for H9_PRO-seq_80_R1_processed.fastq Approx 60% complete for H9_PRO-seq_80_R1_processed.fastq Approx 65% complete for H9_PRO-seq_80_R1_processed.fastq Approx 70% complete for H9_PRO-seq_80_R1_processed.fastq Approx 75% complete for H9_PRO-seq_80_R1_processed.fastq Approx 80% complete for H9_PRO-seq_80_R1_processed.fastq Approx 85% complete for H9_PRO-seq_80_R1_processed.fastq Approx 90% complete for H9_PRO-seq_80_R1_processed.fastq Approx 95% complete for H9_PRO-seq_80_R1_processed.fastq Analysis complete for H9_PRO-seq_80_R1_processed.fastqCommand completed. Elapsed time: 0:00:49. Running peak memory: 3.293GB. PID: 332727; Command: fastqc; Return code: 0; Memory used: 0.181GB > `FastQC report r1` fastqc/H9_PRO-seq_80_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_80/fastq/H9_PRO-seq_80_R1_trimmed.fastq` > `seqkit rmdup --threads 12 --by-seq --ignore-case -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_dedup.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_noadap.fastq` (332789)
[INFO][0m 2112480 duplicated records removedCommand completed. Elapsed time: 0:00:49. Running peak memory: 3.293GB. PID: 332789; Command: seqkit; Return code: 0; Memory used: 2.037GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_dedup.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_trimmed.fastq` (332903,332931)
Command completed. Elapsed time: 0:00:35. Running peak memory: 3.293GB. PID: 332903; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 332931; 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_80/cutadapt/H9_PRO-seq_80_R1_cutadapt.txt | awk '{print $(NF-1)}'` > `Reads_with_adapter` 36677941.0 PEPPRO _RES_ > `grep 'Total basepairs processed:' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/cutadapt/H9_PRO-seq_80_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_80/cutadapt/H9_PRO-seq_80_R1_cutadapt.txt` > `wc -l /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_short.fastq | awk '{print $1}'` > `Uninformative_adapter_reads` 22889260.0 PEPPRO _RES_ > `Duplicate_reads` 2112480.0 PEPPRO _RES_ > `Pct_uninformative_adapter_reads` 49.4503 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/processed_R1.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/processed_R1.flag` (333326)
Command completed. Elapsed time: 0:00:00. Running peak memory: 3.293GB. PID: 333326; 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_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq` > `(cutadapt -j 12 -m 10 -O 1 -a GATCGTCGGACTGTAGAACTCTGAAC /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2.fastq -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_noadap.fastq --too-short-output /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_short.fastq ) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/cutadapt/H9_PRO-seq_80_R2_cutadapt.txt` (333328)
Command completed. Elapsed time: 0:02:02. Running peak memory: 3.417GB. PID: 333328; Command: cutadapt; Return code: 0; Memory used: 3.417GB > `seqtk trimfq -b 8 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_noadap.fastq | seqtk seq -L 10 -r - > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq` (333521,333522)
Command completed. Elapsed time: 0:01:14. Running peak memory: 3.417GB. PID: 333521; Command: seqtk; Return code: 0; Memory used: 0.001GB PID: 333522; Command: seqtk; Return code: 0; Memory used: 0.002GB Evaluating read trimming > `Trimmed_reads` 45330726 PEPPRO _RES_ > `Trim_loss_rate` 51.03 PEPPRO _RES_ Targetless command, running... > `fastqc --noextract --outdir /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq` (333853)
Started analysis of H9_PRO-seq_80_R1_processed.fastq Approx 5% complete for H9_PRO-seq_80_R1_processed.fastq Approx 10% complete for H9_PRO-seq_80_R1_processed.fastq Approx 15% complete for H9_PRO-seq_80_R1_processed.fastq Approx 20% complete for H9_PRO-seq_80_R1_processed.fastq Approx 25% complete for H9_PRO-seq_80_R1_processed.fastq Approx 30% complete for H9_PRO-seq_80_R1_processed.fastq Approx 35% complete for H9_PRO-seq_80_R1_processed.fastq Approx 40% complete for H9_PRO-seq_80_R1_processed.fastq Approx 45% complete for H9_PRO-seq_80_R1_processed.fastq Approx 50% complete for H9_PRO-seq_80_R1_processed.fastq Approx 55% complete for H9_PRO-seq_80_R1_processed.fastq Approx 60% complete for H9_PRO-seq_80_R1_processed.fastq Approx 65% complete for H9_PRO-seq_80_R1_processed.fastq Approx 70% complete for H9_PRO-seq_80_R1_processed.fastq Approx 75% complete for H9_PRO-seq_80_R1_processed.fastq Approx 80% complete for H9_PRO-seq_80_R1_processed.fastq Approx 85% complete for H9_PRO-seq_80_R1_processed.fastq Approx 90% complete for H9_PRO-seq_80_R1_processed.fastq Approx 95% complete for H9_PRO-seq_80_R1_processed.fastq Analysis complete for H9_PRO-seq_80_R1_processed.fastqCommand completed. Elapsed time: 0:00:49. Running peak memory: 3.417GB. PID: 333853; Command: fastqc; Return code: 0; Memory used: 0.18GB > `FastQC report r1` fastqc/H9_PRO-seq_80_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_80/fastqc /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq` (333926)
Started analysis of H9_PRO-seq_80_R2_trimmed.fastq Approx 5% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 10% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 15% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 20% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 25% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 30% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 35% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 40% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 45% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 50% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 55% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 60% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 65% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 70% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 75% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 80% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 85% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 90% complete for H9_PRO-seq_80_R2_trimmed.fastq Approx 95% complete for H9_PRO-seq_80_R2_trimmed.fastq Analysis complete for H9_PRO-seq_80_R2_trimmed.fastqCommand completed. Elapsed time: 0:01:00. Running peak memory: 3.417GB. PID: 333926; Command: fastqc; Return code: 0; Memory used: 0.172GB > `FastQC report r2` fastqc/H9_PRO-seq_80_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_80/cutadapt/H9_PRO-seq_80.hist`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/cutadapt/H9_PRO-seq_80.histogram` > `fastq_pair -t 83317314 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_noadap.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_noadap.fastq` (334042)
Left paired: 23236163 Right paired: 23236163 Left single: 161974 Right single: 2141996 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_noadap.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_noadap.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_noadap.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_noadap.fastq.single.fqCommand completed. Elapsed time: 0:02:42. Running peak memory: 4.556GB. PID: 334042; Command: fastq_pair; Return code: 0; Memory used: 4.556GB > `flash -q -t 12 --compress-prog=pigz --suffix=gz /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_noadap.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_noadap.fastq.paired.fq -o H9_PRO-seq_80 -d /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/cutadapt` (334510)
Command completed. Elapsed time: 0:01:08. Running peak memory: 4.556GB. PID: 334510; Command: flash; Return code: 0; Memory used: 0.12GB ### Plot adapter insertion distribution (06-15 07:41:58) elapsed: 1015.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/cutadapt/H9_PRO-seq_80_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_80/cutadapt/H9_PRO-seq_80.hist -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/cutadapt -u 8` (334714)
Adapter insertion distribution plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 4.556GB. PID: 334714; Command: Rscript; Return code: 0; Memory used: 0.316GB > `Adapter insertion distribution` cutadapt/H9_PRO-seq_80_adapter_insertion_distribution.pdf Adapter insertion distribution cutadapt/H9_PRO-seq_80_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_80/cutadapt/H9_PRO-seq_80.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 07:42:03) elapsed: 5.0 _TIME_ > `awk '{ if (($1-8) == 10) {status = 1}} END {if (status) {print status} else {print 0}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/cutadapt/H9_PRO-seq_80.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_80/cutadapt/H9_PRO-seq_80.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_80/cutadapt/H9_PRO-seq_80.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_80/cutadapt/H9_PRO-seq_80.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_80/cutadapt/H9_PRO-seq_80.hist` > `Degradation_ratio` 1.0312 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed_dups.fastq` > `cp /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed_dups.fastq` (334747)
Command completed. Elapsed time: 0:00:25. Running peak memory: 4.556GB. PID: 334747; 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_80/fastq/processed_R2.flag` > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/processed_R2.flag` (334771)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.556GB. PID: 334771; 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_80/fastq/repaired.flag` > `fastq_pair -t 83317314 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq` (334772)
Left paired: 22486354 Right paired: 22486354 Left single: 179009 Right single: 2199465 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq.single.fqCommand completed. Elapsed time: 0:02:18. Running peak memory: 4.823GB. PID: 334772; Command: fastq_pair; Return code: 0; Memory used: 4.823GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq` (335063)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.823GB. PID: 335063; Command: mv; Return code: 0; Memory used: 0.001GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq` (335065)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.823GB. PID: 335065; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/repaired.flag` (335066)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.823GB. PID: 335066; 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_80/fastq/dups_repaired.flag` > `fastq_pair -t 83317314 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed_dups.fastq` (335067)
Left paired: 20537390 Right paired: 20537390 Left single: 132325 Right single: 4148429 Writing the paired reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_trimmed.fastq.paired.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed_dups.fastq.paired.fq. Writing the single reads to /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_trimmed.fastq.single.fq and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed_dups.fastq.single.fqCommand completed. Elapsed time: 0:01:49. Running peak memory: 4.894GB. PID: 335067; Command: fastq_pair; Return code: 0; Memory used: 4.894GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_trimmed.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_trimmed.fastq` (335354)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 335354; Command: mv; Return code: 0; Memory used: 0.002GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed_dups.fastq.paired.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed_dups.fastq` (335355)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 335355; Command: mv; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/dups_repaired.flag` (335357)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 335357; Command: touch; Return code: 0; Memory used: 0.0GB ### Prealignments (06-15 07:46:37) elapsed: 274.0 _TIME_ Prealignment assemblies: ['human_rDNA'] ### Map to human_rDNA (06-15 07:46:37) elapsed: 0.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/human_rDNA_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/human_rDNA_bt2` (335358)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 335358; 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_80/prealignments/H9_PRO-seq_80_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_80/prealignments/human_rDNA_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_R2.fq` (335359)
> `(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id H9_PRO-seq_80 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_processed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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' 22486354 reads; of these: 22486354 (100.00%) were unpaired; of these: 20155412 (89.63%) aligned 0 times 2330942 (10.37%) aligned exactly 1 time 0 (0.00%) aligned >1 times 10.37% overall alignment rate > `Aligned_reads_human_rDNA` 4661884.0 PEPPRO _RES_ > `Alignment_rate_human_rDNA` 10.28 PEPPRO _RES_ ### Map to human_rDNA (06-15 07:49:26) elapsed: 168.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/human_rDNA_dups_bt2` > `mkfifo /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/human_rDNA_dups_bt2` (335693)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 335693; Command: mkfifo; Return code: 0; Memory used: 0.0GB File not added to cleanup: prealignments/human_rDNA_dups_bt2 Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_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_80/prealignments/human_rDNA_dups_bt2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_trimmed.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R2_trimmed_dups.fastq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_dups_R1.fq /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_dups_R2.fq` (335695)
> `(bowtie2 -p 12 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -x /project/shefflab/genomes/human_rDNA/bowtie2_index/default/human_rDNA --rg-id H9_PRO-seq_80 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/fastq/H9_PRO-seq_80_R1_trimmed.fastq --un /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/human_rDNA_dups_bt2 2>&1 > /dev/null)` not gzipping output 2330942 reads skipped 0 reads lost File not added to cleanup: prealignments/human_rDNA_dups_bt2 ### Map to genome (06-15 07:52:13) elapsed: 167.0 _TIME_ No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_fail_qc_dups.bam Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort.bam` > `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_80 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_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_80/aligned_hg38/tmp2gz8zayr -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp.bam` (336112,336113,336114)
1845871 reads skipped 0 reads lost 20155412 reads; of these: 20155412 (100.00%) were paired; of these: 8354622 (41.45%) aligned concordantly 0 times 9678102 (48.02%) aligned concordantly exactly 1 time 2122688 (10.53%) aligned concordantly >1 times ---- 8354622 pairs aligned concordantly 0 times; of these: 1859562 (22.26%) aligned discordantly 1 time ---- 6495060 pairs aligned 0 times concordantly or discordantly; of these: 12990120 mates make up the pairs; of these: 5331336 (41.04%) aligned 0 times 2799697 (21.55%) aligned exactly 1 time 4859087 (37.41%) aligned >1 times 86.77% overall alignment rate [bam_sort_core] merging from 11 files and 1 in-memory blocks...Command completed. Elapsed time: 0:39:41. Running peak memory: 4.894GB. PID: 336112; Command: bowtie2; Return code: 0; Memory used: 3.773GB PID: 336113; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 336114; Command: samtools; Return code: 0; Memory used: 0.9GB > `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_fail_qc.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort.bam` (340181)
Command completed. Elapsed time: 0:01:12. Running peak memory: 4.894GB. PID: 340181; Command: samtools; Return code: 0; Memory used: 0.018GB > `samtools depth -b /project/shefflab/genomes/hg38/refgene_anno/default/hg38_pre-mRNA.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort.bam | awk '{counter++;sum+=$3}END{print sum/counter}'` > `Mapped_reads` 34979488 PEPPRO _RES_ > `QC_filtered_reads` 20444644 PEPPRO _RES_ > `Aligned_reads` 14534843.5 PEPPRO _RES_ > `Alignment_rate` 32.06 PEPPRO _RES_ > `Total_efficiency` 15.7 PEPPRO _RES_ > `Read_depth` 2.8 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort_dups.bam` > `bowtie2 -p 12 --very-sensitive -X 2000 --rg-id H9_PRO-seq_80 -x /project/shefflab/genomes/hg38/bowtie2_index/default/hg38 --rf -1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_dups_R1.fq -2 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_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_80/aligned_hg38/tmp2gz8zayr -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp_dups.bam` (341287,341293,341294)
18691519 reads; of these: 18691519 (100.00%) were paired; of these: 7582143 (40.56%) aligned concordantly 0 times 9134278 (48.87%) aligned concordantly exactly 1 time 1975098 (10.57%) aligned concordantly >1 times ---- 7582143 pairs aligned concordantly 0 times; of these: 1760249 (23.22%) aligned discordantly 1 time ---- 5821894 pairs aligned 0 times concordantly or discordantly; of these: 11643788 mates make up the pairs; of these: 4858981 (41.73%) aligned 0 times 2643468 (22.70%) aligned exactly 1 time 4141339 (35.57%) aligned >1 times 87.00% overall alignment rate [bam_sort_core] merging from 10 files and 1 in-memory blocks...Command completed. Elapsed time: 0:33:00. Running peak memory: 4.894GB. PID: 341293; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 341287; Command: bowtie2; Return code: 0; Memory used: 3.772GB PID: 341294; Command: samtools; Return code: 0; Memory used: 0.898GB > `samtools view -q 10 -b -@ 12 -U /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_fail_qc_dups.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp_dups.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort_dups.bam` (344597)
Command completed. Elapsed time: 0:01:09. Running peak memory: 4.894GB. PID: 344597; Command: samtools; Return code: 0; Memory used: 0.018GB ### Compress all unmapped read files (06-15 09:18:23) elapsed: 5171.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_R2.fq.gz` > `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_R2.fq` (344674)
Command completed. Elapsed time: 0:00:18. Running peak memory: 4.894GB. PID: 344674; Command: pigz; Return code: 0; Memory used: 0.011GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_R1.fq.gz` > `pigz -f -p 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/prealignments/H9_PRO-seq_80_human_rDNA_unmap_R1.fq` (344704)
Command completed. Elapsed time: 0:00:21. Running peak memory: 4.894GB. PID: 344704; Command: pigz; Return code: 0; Memory used: 0.013GB Missing stat 'Mitochondrial_reads' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp.bam` (344738)
Command completed. Elapsed time: 0:00:30. Running peak memory: 4.894GB. PID: 344738; Command: samtools; Return code: 0; Memory used: 0.012GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp.bam | grep -we 'chrM' -we 'chrMT' -we 'M' -we 'MT' -we 'rCRSd' -we 'rCRSd_3k'| cut -f 3` > `Mitochondrial_reads` 672784 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_noMT.bam` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort.bam` (344767)
Command completed. Elapsed time: 0:00:22. Running peak memory: 4.894GB. PID: 344767; Command: samtools; Return code: 0; Memory used: 0.014GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_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_80/aligned_hg38/chr_sizes.bed` (344787,344788,344789,344790)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 344788; Command: cut; Return code: 0; Memory used: 0.0GB PID: 344790; Command: grep; Return code: 0; Memory used: 0.0GB PID: 344787; Command: samtools; Return code: 0; Memory used: 0.011GB PID: 344789; 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_80/aligned_hg38/chr_sizes.bed -b -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_noMT.bam` (344792)
Command completed. Elapsed time: 0:00:28. Running peak memory: 4.894GB. PID: 344792; Command: samtools; Return code: 0; Memory used: 0.019GB > `mv /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_noMT.bam /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort.bam` (345066)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 345066; Command: mv; Return code: 0; Memory used: 0.001GB > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort.bam` (345068)
Command completed. Elapsed time: 0:00:22. Running peak memory: 4.894GB. PID: 345068; Command: samtools; Return code: 0; Memory used: 0.013GB ### Split BAM file (06-15 09:20:46) elapsed: 143.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam` (345087,345088)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:02:05. Running peak memory: 4.894GB. PID: 345087; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 345088; Command: samtools; Return code: 0; Memory used: 4.156GB > `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE2.bam` (345232,345233)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:43. Running peak memory: 4.894GB. PID: 345232; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 345233; Command: samtools; Return code: 0; Memory used: 3.33GB Missing stat 'Maximum_read_length' > `samtools stats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_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_80/aligned_hg38/H9_PRO-seq_80_temp_dups.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp_dups.bam` (345595)
Command completed. Elapsed time: 0:00:28. Running peak memory: 4.894GB. PID: 345595; Command: samtools; Return code: 0; Memory used: 0.013GB > `samtools idxstats /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_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_80/aligned_hg38/H9_PRO-seq_80_sort_dups.bam` No files match cleanup pattern: /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort_dups.bam.bai Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_dups_PE1.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_dups_PE2.bam` > `samtools view -b -f 64 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_dups_PE1.bam` (345623,345624)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:02:00. Running peak memory: 4.894GB. PID: 345623; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 345624; Command: samtools; Return code: 0; Memory used: 3.997GB > `samtools view -b -f 128 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_sort_dups.bam | samtools sort - -@ 12 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_dups_PE2.bam` (345768,345769)
[bam_sort_core] merging from 0 files and 12 in-memory blocks...Command completed. Elapsed time: 0:01:40. Running peak memory: 4.894GB. PID: 345768; Command: samtools; Return code: 0; Memory used: 0.004GB PID: 345769; Command: samtools; Return code: 0; Memory used: 3.21GB ### Calculate library complexity (06-15 09:29:28) elapsed: 522.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_preseq_out.txt` > `preseq c_curve -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_preseq_out.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_dups_PE1.bam` (345890)
BAM_INPUT TOTAL READS = 14983475 COUNTS_SUM = 14983475 DISTINCT READS = 1.23124e+07 DISTINCT COUNTS = 284 MAX COUNT = 22754 COUNTS OF 1 = 1.10363e+07 OBSERVED COUNTS (22755) 1 11036268 2 873369 3 200465 4 78869 5 39923 6 23143 7 14523 8 9658 9 6943 10 5057 11 3773 12 2955 13 2220 14 1753 15 1498 16 1200 17 1075 18 884 19 794 20 658 21 562 22 518 23 441 24 404 25 329 26 321 27 289 28 282 29 236 30 224 31 176 32 185 33 177 34 132 35 123 36 153 37 135 38 109 39 113 40 109 41 95 42 88 43 94 44 75 45 90 46 67 47 79 48 74 49 61 50 66 51 52 52 55 53 44 54 39 55 43 56 49 57 34 58 37 59 46 60 34 61 29 62 24 63 37 64 22 65 26 66 33 67 27 68 34 69 26 70 26 71 26 72 19 73 22 74 16 75 18 76 21 77 20 78 16 79 21 80 13 81 22 82 17 83 14 84 14 85 13 86 13 87 5 88 11 89 14 90 10 91 6 92 11 93 13 94 14 95 6 96 9 97 9 98 10 99 12 100 7 101 11 102 7 103 8 104 3 105 7 106 4 107 5 108 10 109 11 110 8 111 6 112 10 113 4 114 8 115 6 116 7 117 4 118 4 119 5 120 2 121 10 122 2 123 5 124 3 125 3 126 3 127 7 128 7 129 6 130 4 131 5 132 3 133 2 134 2 135 2 136 2 137 6 138 6 139 2 140 2 141 5 142 2 143 2 144 3 145 6 146 4 147 3 148 3 149 1 153 1 154 4 155 1 156 2 157 1 158 2 159 1 160 2 161 4 162 2 163 2 164 7 165 7 166 3 168 1 169 3 170 3 171 1 172 3 173 1 174 1 175 2 177 2 178 1 179 3 180 2 181 1 182 2 183 2 184 4 186 1 188 6 189 3 192 1 194 1 195 2 196 1 198 2 201 1 203 2 205 1 206 1 207 1 209 1 210 1 214 2 215 1 217 2 218 1 219 2 220 1 222 2 223 1 224 1 226 1 227 1 228 1 230 1 232 1 233 1 243 1 244 1 248 2 252 2 253 1 254 2 256 1 257 2 259 3 261 1 264 1 265 2 269 2 272 1 274 1 275 2 277 1 281 1 282 1 285 1 292 1 294 2 303 1 304 1 307 1 309 1 311 1 315 1 316 1 327 1 334 1 346 1 351 1 355 1 361 1 378 1 395 1 397 1 406 1 410 1 412 1 418 1 420 1 430 1 443 1 446 1 479 1 555 1 567 1 569 2 571 1 579 1 583 1 716 1 719 1 741 1 786 1 815 1 956 1 1013 1 1067 1 1304 1 1532 1 1541 1 1558 1 1869 1 1983 1 2093 1 2831 1 3629 1 7419 1 8643 1 11051 1 20426 1 22754 1 sample size: 1000000 sample size: 2000000 sample size: 3000000 sample size: 4000000 sample size: 5000000 sample size: 6000000 sample size: 7000000 sample size: 8000000 sample size: 9000000 sample size: 10000000 sample size: 11000000 sample size: 12000000 sample size: 13000000 sample size: 14000000Command completed. Elapsed time: 0:01:23. Running peak memory: 4.894GB. PID: 345890; 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_80/QC_hg38/H9_PRO-seq_80_preseq_yield.txt` > `preseq lc_extrap -v -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_preseq_yield.txt -B /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_dups_PE1.bam` (346215)
BAM_INPUT TOTAL READS = 14983475 DISTINCT READS = 1.23124e+07 DISTINCT COUNTS = 284 MAX COUNT = 22754 COUNTS OF 1 = 1.10363e+07 MAX TERMS = 100 OBSERVED COUNTS (22755) 1 11036268 2 873369 3 200465 4 78869 5 39923 6 23143 7 14523 8 9658 9 6943 10 5057 11 3773 12 2955 13 2220 14 1753 15 1498 16 1200 17 1075 18 884 19 794 20 658 21 562 22 518 23 441 24 404 25 329 26 321 27 289 28 282 29 236 30 224 31 176 32 185 33 177 34 132 35 123 36 153 37 135 38 109 39 113 40 109 41 95 42 88 43 94 44 75 45 90 46 67 47 79 48 74 49 61 50 66 51 52 52 55 53 44 54 39 55 43 56 49 57 34 58 37 59 46 60 34 61 29 62 24 63 37 64 22 65 26 66 33 67 27 68 34 69 26 70 26 71 26 72 19 73 22 74 16 75 18 76 21 77 20 78 16 79 21 80 13 81 22 82 17 83 14 84 14 85 13 86 13 87 5 88 11 89 14 90 10 91 6 92 11 93 13 94 14 95 6 96 9 97 9 98 10 99 12 100 7 101 11 102 7 103 8 104 3 105 7 106 4 107 5 108 10 109 11 110 8 111 6 112 10 113 4 114 8 115 6 116 7 117 4 118 4 119 5 120 2 121 10 122 2 123 5 124 3 125 3 126 3 127 7 128 7 129 6 130 4 131 5 132 3 133 2 134 2 135 2 136 2 137 6 138 6 139 2 140 2 141 5 142 2 143 2 144 3 145 6 146 4 147 3 148 3 149 1 153 1 154 4 155 1 156 2 157 1 158 2 159 1 160 2 161 4 162 2 163 2 164 7 165 7 166 3 168 1 169 3 170 3 171 1 172 3 173 1 174 1 175 2 177 2 178 1 179 3 180 2 181 1 182 2 183 2 184 4 186 1 188 6 189 3 192 1 194 1 195 2 196 1 198 2 201 1 203 2 205 1 206 1 207 1 209 1 210 1 214 2 215 1 217 2 218 1 219 2 220 1 222 2 223 1 224 1 226 1 227 1 228 1 230 1 232 1 233 1 243 1 244 1 248 2 252 2 253 1 254 2 256 1 257 2 259 3 261 1 264 1 265 2 269 2 272 1 274 1 275 2 277 1 281 1 282 1 285 1 292 1 294 2 303 1 304 1 307 1 309 1 311 1 315 1 316 1 327 1 334 1 346 1 351 1 355 1 361 1 378 1 395 1 397 1 406 1 410 1 412 1 418 1 420 1 430 1 443 1 446 1 479 1 555 1 567 1 569 2 571 1 579 1 583 1 716 1 719 1 741 1 786 1 815 1 956 1 1013 1 1067 1 1304 1 1532 1 1541 1 1558 1 1869 1 1983 1 2093 1 2831 1 3629 1 7419 1 8643 1 11051 1 20426 1 22754 1 [ESTIMATING YIELD CURVE] [BOOTSTRAPPING HISTOGRAM] ..........................._...................................._..................................... [COMPUTING CONFIDENCE INTERVALS] [WRITING OUTPUT]Command completed. Elapsed time: 0:01:30. Running peak memory: 4.894GB. PID: 346215; 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_80/QC_hg38/H9_PRO-seq_80_preseq_counts.txt` > `echo '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_preseq_yield.txt '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_dups_PE1.bam)' '$(samtools view -c -F 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam) > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_preseq_counts.txt` (346289)
Command completed. Elapsed time: 0:00:22. Running peak memory: 4.894GB. PID: 346289; 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_80/QC_hg38/H9_PRO-seq_80_preseq_plot.pdf`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_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_80/QC_hg38/H9_PRO-seq_80_preseq_yield.txt -r /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_preseq_counts.txt -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_preseq_plot` (346314)
Processing H9_PRO-seq_80 INFO: Found real counts for H9_PRO-seq_80 - Total (M): 15.588108 Unique (M): 14.983475 Library complexity plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 4.894GB. PID: 346314; Command: Rscript; Return code: 0; Memory used: 0.316GB > `Library complexity` QC_hg38/H9_PRO-seq_80_preseq_plot.pdf Library complexity QC_hg38/H9_PRO-seq_80_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_80/QC_hg38/H9_PRO-seq_80_preseq_yield.txt | awk '{print $2}'` > `Frac_exp_unique_at_10M` 0.8537 PEPPRO _RES_ ### Calculate NRF, PBC1, and PBC2 (06-15 09:32:48) elapsed: 200.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam.bai` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam` (346333)
Command completed. Elapsed time: 0:00:12. Running peak memory: 4.894GB. PID: 346333; Command: samtools; Return code: 0; Memory used: 0.008GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_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_80/aligned_hg38/H9_PRO-seq_80_PE1.bam -c 12 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_bamQC.tsv` (346344)
Configured logger 'root' using pararead v0.6 Registering input file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam' Temporary files will be stored in: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/tmp_H9_PRO-seq_80_PE1_5q6gvnk9' Processing with 12 cores... Discarding 101 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr14_GL000009v2_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270755v1'] Keeping 94 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270509v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV']Command completed. Elapsed time: 0:00:13. Running peak memory: 4.894GB. PID: 346344; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamQC.py; Return code: 0; Memory used: 1.548GB > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "NRF") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC1") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_bamQC.tsv` > `awk '{ for (i=1; i<=NF; ++i) { if ($i ~ "PBC2") c=i } getline; print $c }' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_bamQC.tsv` > `NRF` 1.0 PEPPRO _RES_ > `PBC1` 7794054.0 PEPPRO _RES_ > `PBC2` 7794054.0 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_unmap.bam` > `samtools view -b -@ 12 -f 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_unmap.bam` (346385)
Command completed. Elapsed time: 0:00:07. Running peak memory: 4.894GB. PID: 346385; Command: samtools; Return code: 0; Memory used: 0.009GB > `samtools view -c -f 4 -@ 12 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_temp.bam` > `Unmapped_reads` 5331336 PEPPRO _RES_ ### Split BAM by strand (06-15 09:33:25) elapsed: 37.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam` > `samtools view -bh -F 20 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam` (346428)
Command completed. Elapsed time: 0:00:54. Running peak memory: 4.894GB. PID: 346428; 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_80/aligned_hg38/H9_PRO-seq_80_PE1.bam > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam` (346474)
Command completed. Elapsed time: 0:00:52. Running peak memory: 4.894GB. PID: 346474; Command: samtools; Return code: 0; Memory used: 0.006GB ### Calculate TSS enrichment (06-15 09:35:11) elapsed: 106.0 _TIME_ Missing stat 'TSS_non-coding_score' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/plus_TSS.tsv`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/minus_TSS.tsv` > `sed -n -e '/[[:space:]]+/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/plus_TSS.tsv' -e '/[[:space:]]-/w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/minus_TSS.tsv' /project/shefflab/genomes/hg38/refgene_anno/default/hg38_TSS.bed` (346707)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 346707; 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_80/QC_hg38/H9_PRO-seq_80_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_80/aligned_hg38/H9_PRO-seq_80_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/plus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_plus_TssEnrichment.txt` (346708)
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.894GB. PID: 346708; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.974GB > `TSS_coding_score` 33.8 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_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_80/aligned_hg38/H9_PRO-seq_80_PE1.bam -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/minus_TSS.tsv -p ends -c 12 -z -v -s 6 -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_minus_TssEnrichment.txt` (346739)
Command completed. Elapsed time: 0:00:04. Running peak memory: 4.894GB. PID: 346739; Command: /scratch/jps3dp/tools/databio//peppro/tools/pyTssEnrichment.py; Return code: 0; Memory used: 0.992GB > `TSS_non-coding_score` 12.3 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_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_80/QC_hg38/H9_PRO-seq_80_plus_TssEnrichment.txt /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_minus_TssEnrichment.txt` (346770)
Generating TSS plot with /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_plus_TssEnrichment.txt and /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_minus_TssEnrichment.txt `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' `geom_smooth()` using formula 'y ~ x' TSS enrichment plot completed!Command completed. Elapsed time: 0:00:06. Running peak memory: 4.894GB. PID: 346770; Command: Rscript; Return code: 0; Memory used: 0.321GB > `TSS enrichment` QC_hg38/H9_PRO-seq_80_TSSenrichment.pdf TSS enrichment QC_hg38/H9_PRO-seq_80_TSSenrichment.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt` > `samtools view -H /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_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_80/QC_hg38/chr_order.txt` (346792,346793,346794,346795)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 346792; Command: samtools; Return code: 0; Memory used: 0.0GB PID: 346794; Command: awk; Return code: 0; Memory used: 0.0GB PID: 346793; Command: grep; Return code: 0; Memory used: 0.0GB PID: 346795; 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_80/QC_hg38/chr_keep.txt` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_keep.txt` (346797)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 346797; Command: cut; Return code: 0; Memory used: 0.0GB ### Calculate Pause Index (PI) (06-15 09:35:27) elapsed: 16.0 _TIME_ Missing stat 'Pause_index' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_ensembl_tss.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_ensembl_gene_body.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_ensembl_tss.bed` (346799,346800)
Command completed. Elapsed time: 0:00:02. Running peak memory: 4.894GB. PID: 346799; Command: grep; Return code: 0; Memory used: 0.004GB PID: 346800; Command: bedtools; Return code: 0; Memory used: 0.098GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_ensembl_gene_body.bed` (346804,346805)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 346804; Command: grep; Return code: 0; Memory used: 0.003GB PID: 346805; Command: bedtools; Return code: 0; Memory used: 0.004GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_TSS_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_ensembl_tss.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/H9_PRO-seq_80_TSS_density.bed` (346807,346808,346809,346810)
Command completed. Elapsed time: 0:00:21. Running peak memory: 4.894GB. PID: 346807; Command: bedtools; Return code: 0; Memory used: 0.009GB PID: 346809; Command: sort; Return code: 0; Memory used: 0.012GB PID: 346808; Command: awk; Return code: 0; Memory used: 0.001GB PID: 346810; Command: sort; Return code: 0; Memory used: 0.003GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_gene_body_density.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_ensembl_gene_body.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt | awk '$7>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_gene_body_density.bed` (346830,346831,346832)
Command completed. Elapsed time: 0:00:23. Running peak memory: 4.894GB. PID: 346831; Command: awk; Return code: 0; Memory used: 0.001GB PID: 346830; Command: bedtools; Return code: 0; Memory used: 0.084GB PID: 346832; Command: sort; Return code: 0; Memory used: 0.003GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_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_80/QC_hg38/H9_PRO-seq_80_TSS_density.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_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_80/QC_hg38/tmp3j3go7g0` (346854,346855,346856)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 346854; Command: join; Return code: 0; Memory used: 0.001GB PID: 346856; Command: env; Return code: 0; Memory used: 0.006GB PID: 346855; 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_80/QC_hg38/tmp3j3go7g0 | 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_80/QC_hg38/H9_PRO-seq_80_pause_index.bed` > `awk -v OFS=' ' '{ if ($5 > 0.0155008) {print $1, $2, $3, $4, $6, $7}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/tmp3j3go7g0 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_pause_index.bed` (346862)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 346862; 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_80/QC_hg38/H9_PRO-seq_80_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` 33.72 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_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_80/QC_hg38/H9_PRO-seq_80_pause_index.bed` (346867)
Pause index plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 4.894GB. PID: 346867; Command: Rscript; Return code: 0; Memory used: 0.319GB > `Pause index` QC_hg38/H9_PRO-seq_80_pause_index.pdf Pause index QC_hg38/H9_PRO-seq_80_pause_index.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_pause_index.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_pause_index.bed` (346888)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 346888; Command: pigz; Return code: 0; Memory used: 0.004GB ### Calculate Fraction of Reads in pre-mature mRNA (06-15 09:36:19) elapsed: 52.0 _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_80/aligned_hg38/H9_PRO-seq_80_plus.bam` 14534843.5 5639799 > `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_80/aligned_hg38/H9_PRO-seq_80_minus.bam` 14534843.5 5259266 > `Minus_FRiP` 0.36 PEPPRO _RES_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_gene_coverage.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_gene_sort.bed` (346927,346928)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 346927; Command: grep; Return code: 0; Memory used: 0.004GB PID: 346928; 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_80/QC_hg38/hg38_gene_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_gene_coverage.bed` (346931)
Command completed. Elapsed time: 0:00:24. Running peak memory: 4.894GB. PID: 346931; Command: bedtools; Return code: 0; Memory used: 0.085GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/raw/hg38_annotations.bed.gz` (346969)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 346969; Command: ln; Return code: 0; Memory used: 0.0GB > `pigz -f -p 12 -d -c /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/hg38_annotations.bed.gz > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/hg38_annotations.bed` (346970)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 346970; Command: pigz; Return code: 0; Memory used: 0.002GB ### Calculate cumulative and terminal fraction of reads in features (cFRiF/FRiF) (06-15 09:37:11) elapsed: 53.0 _TIME_ > `cut -f 4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/hg38_annotations.bed | sort -u` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Enhancer` > `awk -F' ' '{print>"/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/"$4}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/raw/hg38_annotations.bed` (346978)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 346978; 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_80/QC_hg38/Enhancer_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Enhancer_sort.bed` (346981,346982,346983,346984)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 346981; Command: cut; Return code: 0; Memory used: 0.0GB PID: 346982; Command: grep; Return code: 0; Memory used: 0.002GB PID: 346984; Command: bedtools; Return code: 0; Memory used: 0.047GB PID: 346983; 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_80/QC_hg38/H9_PRO-seq_80_Enhancer_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Enhancer_plus_coverage.bed` (346987)
Command completed. Elapsed time: 0:00:10. Running peak memory: 4.894GB. PID: 346987; 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_80/QC_hg38/H9_PRO-seq_80_Enhancer_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Enhancer_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Enhancer_minus_coverage.bed` (346997)
Command completed. Elapsed time: 0:00:10. Running peak memory: 4.894GB. PID: 346997; Command: bedtools; Return code: 0; Memory used: 0.009GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter_sort.bed` (347007,347008,347009,347010)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 347007; Command: cut; Return code: 0; Memory used: 0.0GB PID: 347008; Command: grep; Return code: 0; Memory used: 0.003GB PID: 347010; Command: bedtools; Return code: 0; Memory used: 0.008GB PID: 347009; 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_80/QC_hg38/H9_PRO-seq_80_Promoter_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_plus_coverage.bed` (347013)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.894GB. PID: 347013; Command: bedtools; Return code: 0; Memory used: 0.02GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_minus_coverage.bed` (347024)
Command completed. Elapsed time: 0:00:10. Running peak memory: 4.894GB. PID: 347024; Command: bedtools; Return code: 0; Memory used: 0.016GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter Flanking Region` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter_Flanking_Region` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter Flanking Region" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter_Flanking_Region"` (347034)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 347034; 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_80/QC_hg38/Promoter_Flanking_Region_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter_Flanking_Region_sort.bed` (347035,347036,347037,347038)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 347035; Command: cut; Return code: 0; Memory used: 0.0GB PID: 347037; Command: cut; Return code: 0; Memory used: 0.001GB PID: 347036; Command: grep; Return code: 0; Memory used: 0.002GB PID: 347038; Command: bedtools; Return code: 0; Memory used: 0.01GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_Flanking_Region_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_Flanking_Region_plus_coverage.bed` (347041)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.894GB. PID: 347041; 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_80/QC_hg38/H9_PRO-seq_80_Promoter_Flanking_Region_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Promoter_Flanking_Region_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_Flanking_Region_minus_coverage.bed` (347051)
Command completed. Elapsed time: 0:00:10. Running peak memory: 4.894GB. PID: 347051; Command: bedtools; Return code: 0; Memory used: 0.009GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/5' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/5_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/5' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/5_UTR"` (347061)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 347061; 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_80/QC_hg38/5_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/5_UTR_sort.bed` (347062,347063,347064,347065)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 347062; Command: cut; Return code: 0; Memory used: 0.0GB PID: 347063; Command: grep; Return code: 0; Memory used: 0.003GB PID: 347065; Command: bedtools; Return code: 0; Memory used: 0.01GB PID: 347064; 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_80/QC_hg38/H9_PRO-seq_80_5_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_5_UTR_plus_coverage.bed` (347068)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.894GB. PID: 347068; 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_80/QC_hg38/H9_PRO-seq_80_5_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/5_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_5_UTR_minus_coverage.bed` (347095)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.894GB. PID: 347095; Command: bedtools; Return code: 0; Memory used: 0.01GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/3' UTR` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/3_UTR` > `mv "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/3' UTR" "/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/3_UTR"` (347107)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 347107; 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_80/QC_hg38/3_UTR_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/3_UTR_sort.bed` (347108,347109,347110,347111)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 347108; Command: cut; Return code: 0; Memory used: 0.0GB PID: 347109; Command: grep; Return code: 0; Memory used: 0.003GB PID: 347111; Command: bedtools; Return code: 0; Memory used: 0.01GB PID: 347110; 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_80/QC_hg38/H9_PRO-seq_80_3_UTR_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_3_UTR_plus_coverage.bed` (347128)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.894GB. PID: 347128; Command: bedtools; Return code: 0; Memory used: 0.011GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_3_UTR_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/3_UTR_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_3_UTR_minus_coverage.bed` (347140)
Command completed. Elapsed time: 0:00:10. Running peak memory: 4.894GB. PID: 347140; Command: bedtools; Return code: 0; Memory used: 0.009GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Exon` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Exon_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Exon_sort.bed` (347150,347151,347152,347153)
Command completed. Elapsed time: 0:00:03. Running peak memory: 4.894GB. PID: 347150; Command: cut; Return code: 0; Memory used: 0.0GB PID: 347151; Command: grep; Return code: 0; Memory used: 0.004GB PID: 347153; Command: bedtools; Return code: 0; Memory used: 0.171GB PID: 347152; 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_80/QC_hg38/H9_PRO-seq_80_Exon_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Exon_plus_coverage.bed` (347159)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.894GB. PID: 347159; Command: bedtools; Return code: 0; Memory used: 0.02GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Exon_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Exon_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Exon_minus_coverage.bed` (347204)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.894GB. PID: 347204; Command: bedtools; Return code: 0; Memory used: 0.013GB Target exists: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Intron` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Intron_sort.bed` > `cut -f 1 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt | grep -wf - /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Intron_sort.bed` (347216,347217,347218,347219)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 347216; Command: cut; Return code: 0; Memory used: 0.0GB PID: 347218; Command: cut; Return code: 0; Memory used: 0.001GB PID: 347217; Command: grep; Return code: 0; Memory used: 0.002GB PID: 347219; Command: bedtools; Return code: 0; Memory used: 0.083GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Intron_plus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Intron_plus_coverage.bed` (347222)
Command completed. Elapsed time: 0:00:12. Running peak memory: 4.894GB. PID: 347222; Command: bedtools; Return code: 0; Memory used: 0.024GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Intron_minus_coverage.bed` > `bedtools coverage -sorted -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/Intron_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Intron_minus_coverage.bed` (347239)
Command completed. Elapsed time: 0:00:11. Running peak memory: 4.894GB. PID: 347239; Command: bedtools; Return code: 0; Memory used: 0.03GB ### Plot cFRiF/FRiF (06-15 09:39:52) elapsed: 161.0 _TIME_ > `samtools view -@ 12 -q 10 -c -F4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam` Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_cFRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_80 -z 3099922541 -n 7955869 -y cfrif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_cFRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Intron_plus_coverage.bed` (347266)
Cumulative cfrif plot completed!Command completed. Elapsed time: 0:00:34. Running peak memory: 4.894GB. PID: 347266; Command: Rscript; Return code: 0; Memory used: 0.484GB > `cFRiF` QC_hg38/H9_PRO-seq_80_cFRiF.pdf cFRiF QC_hg38/H9_PRO-seq_80_cFRiF.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_FRiF.pdf` > `Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO.R frif -s H9_PRO-seq_80 -z 3099922541 -n 7955869 -y frif --reads -o /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_FRiF.pdf --bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Enhancer_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Promoter_Flanking_Region_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_5_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_3_UTR_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Exon_plus_coverage.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_Intron_plus_coverage.bed` (347560)
Cumulative frif plot completed!Command completed. Elapsed time: 0:00:25. Running peak memory: 4.894GB. PID: 347560; Command: Rscript; Return code: 0; Memory used: 0.484GB > `FRiF` QC_hg38/H9_PRO-seq_80_FRiF.pdf FRiF QC_hg38/H9_PRO-seq_80_FRiF.png PEPPRO _OBJ_ ### Calculate mRNA contamination (06-15 09:40:52) elapsed: 60.0 _TIME_ Missing stat 'mRNA_contamination' Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_exons_sort.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_introns_sort.bed` > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_exons_sort.bed` (347596,347597)
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.894GB. PID: 347597; Command: bedtools; Return code: 0; Memory used: 0.094GB PID: 347596; Command: grep; Return code: 0; Memory used: 0.004GB > `grep -wf /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/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_80/QC_hg38/chr_order.txt | bedtools sort -i stdin -faidx /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_introns_sort.bed` (347619,347620,347621)
Command completed. Elapsed time: 0:00:05. Running peak memory: 4.894GB. PID: 347619; Command: grep; Return code: 0; Memory used: 0.005GB PID: 347621; Command: bedtools; Return code: 0; Memory used: 0.004GB PID: 347620; Command: bedtools; Return code: 0; Memory used: 0.034GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_exons_coverage.bed`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_introns_coverage.bed` > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_exons_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_exons_coverage.bed` (347627)
Command completed. Elapsed time: 0:00:20. Running peak memory: 4.894GB. PID: 347627; Command: bedtools; Return code: 0; Memory used: 0.014GB > `bedtools coverage -sorted -counts -s -a /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/hg38_introns_sort.bed -b /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_PE1.bam -g /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/chr_order.txt > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_introns_coverage.bed` (347645)
Command completed. Elapsed time: 0:00:22. Running peak memory: 4.894GB. PID: 347645; Command: bedtools; Return code: 0; Memory used: 0.073GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_exons_rpkm.bed` > `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/14.5348435)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_exons_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_exons_rpkm.bed` (347665,347666,347667)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 347665; Command: awk; Return code: 0; Memory used: 0.007GB PID: 347667; Command: sort; Return code: 0; Memory used: 0.007GB PID: 347666; 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_80/QC_hg38/H9_PRO-seq_80_introns_rpkm.bed` > `awk -v OFS=' ' '{chrom[$4] = $1; if($4!=prev4) {chromStart[$4] = $2} strand[$4] = $6; readCount[$4] += $7; exonCount[$4] += 1; geneSizeKB[$4] += (sqrt(($3-$2+0.00000001)^2)/1000); gene[$4] = $4; chromEnd[$4]=$3; prev4=$4} END { for (a in readCount) { print chrom[a], chromStart[a], chromEnd[a], gene[a], (readCount[a]/14.5348435)/geneSizeKB[a], strand[a]}}' /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_introns_coverage.bed | awk '$5>0' | sort -k4 > /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_introns_rpkm.bed` (347669,347670,347671)
Command completed. Elapsed time: 0:00:01. Running peak memory: 4.894GB. PID: 347669; Command: awk; Return code: 0; Memory used: 0.007GB PID: 347671; Command: sort; Return code: 0; Memory used: 0.004GB PID: 347670; 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_80/QC_hg38/H9_PRO-seq_80_exon_intron_ratios.bed` > `join --nocheck-order -a1 -a2 -j4 /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_introns_rpkm.bed /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_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_80/QC_hg38/H9_PRO-seq_80_exon_intron_ratios.bed` (347674,347675,347676)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 347674; Command: join; Return code: 0; Memory used: 0.001GB PID: 347676; Command: sort; Return code: 0; Memory used: 0.004GB PID: 347675; 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_80/QC_hg38/H9_PRO-seq_80_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_80/QC_hg38/H9_PRO-seq_80_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_80/QC_hg38/H9_PRO-seq_80_exon_intron_ratios.bed --annotate` (347682)
mRNA contamination plot completed!Command completed. Elapsed time: 0:00:05. Running peak memory: 4.894GB. PID: 347682; Command: Rscript; Return code: 0; Memory used: 0.321GB > `mRNA contamination` QC_hg38/H9_PRO-seq_80_mRNA_contamination.pdf mRNA contamination QC_hg38/H9_PRO-seq_80_mRNA_contamination.png PEPPRO _OBJ_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_exon_intron_ratios.bed.gz` > `pigz -f -p 12 -f /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/QC_hg38/H9_PRO-seq_80_exon_intron_ratios.bed` (347702)
Command completed. Elapsed time: 0:00:00. Running peak memory: 4.894GB. PID: 347702; Command: pigz; Return code: 0; Memory used: 0.005GB ### Produce bigWig files (06-15 09:41:50) elapsed: 58.0 _TIME_ Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_plus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_plus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_plus.bam` (347711)
Command completed. Elapsed time: 0:00:06. Running peak memory: 4.894GB. PID: 347711; Command: samtools; Return code: 0; Memory used: 0.01GB > `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_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_80/signal_hg38/H9_PRO-seq_80_plus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_plus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 14534843.5` (347716)
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_80/aligned_hg38/H9_PRO-seq_80_plus.bam' Temporary files will be stored in: 'tmp_H9_PRO-seq_80_plus_cuttrace_konb2rr9' Processing with 4 cores... stdin is empty of data Discarding 113 chunk(s) of reads: ['chrM', 'chr1_KI270707v1_random', 'chr1_KI270710v1_random', 'chr2_KI270715v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr14_GL000009v2_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_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_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000226v1', 'chrUn_KI270746v1', 'chrUn_KI270749v1', 'chrUn_KI270753v1', 'chrUn_KI270755v1', 'chrUn_KI270757v1'] Keeping 82 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270519v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 82 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_plus_exact_body_0-mer.bw' Merging 82 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_plus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:07:16. Running peak memory: 4.894GB. PID: 347716; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.768GB Target to produce: `/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_minus_exact_body_0-mer.bw`,`/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_minus_smooth_body_0-mer.bw` > `samtools index /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_minus.bam` (349251)
Command completed. Elapsed time: 0:00:06. Running peak memory: 4.894GB. PID: 349251; Command: samtools; Return code: 0; Memory used: 0.011GB > `/scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py -i /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/aligned_hg38/H9_PRO-seq_80_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_80/signal_hg38/H9_PRO-seq_80_minus_exact_body_0-mer.bw -w /project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_minus_smooth_body_0-mer.bw -p 8 --variable-step --tail-edge --scale 14534843.5` (349257)
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_80/aligned_hg38/H9_PRO-seq_80_minus.bam' Temporary files will be stored in: 'tmp_H9_PRO-seq_80_minus_cuttrace_tx0_9dvj' Processing with 4 cores... stdin is empty of data Discarding 113 chunk(s) of reads: ['chrM', 'chr1_KI270710v1_random', 'chr1_KI270712v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr4_GL000008v2_random', 'chr9_KI270717v1_random', 'chr14_GL000009v2_random', 'chr14_KI270723v1_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270732v1_random', 'chr22_KI270735v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_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_KI270755v1'] Keeping 82 chunk(s) of reads: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270711v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr3_GL000221v1_random', 'chr5_GL000208v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr22_KI270731v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chrUn_KI270442v1', 'chrUn_KI270438v1', 'chrUn_KI270509v1', 'chrUn_KI270538v1', 'chrUn_KI270589v1', 'chrUn_KI270593v1', 'chrUn_KI270333v1', 'chrUn_KI270337v1', 'chrUn_KI270362v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chrEBV'] Reduce step (merge files)... Merging 82 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_minus_exact_body_0-mer.bw' Merging 82 files into output file: '/project/shefflab/processed/peppro/paper/6.11.2020/results_pipeline/H9_PRO-seq_80/signal_hg38/H9_PRO-seq_80_minus_smooth_body_0-mer.bw'Command completed. Elapsed time: 0:07:11. Running peak memory: 4.894GB. PID: 349257; Command: /scratch/jps3dp/tools/databio//peppro/tools/bamSitesToWig.py; Return code: 0; Memory used: 2.34GB ### Pipeline completed. Epilogue * Elapsed time (this run): 2:39:05 * Total elapsed time (all runs): 4:36:50 * Peak memory (this run): 4.8945 GB * Pipeline completed time: 2020-06-15 09:56:30