Pipeline run code and environment:

  • Command: /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/pipelines/pepatac_collator.py --config /sfs/lustre/bahamut/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/tutorial/tutorial.yaml -O /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/ -P 1 -M 16000 -n PEPATAC_tutorial -r /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline
  • Compute host: udc-ba35-36
  • Working dir: /sfs/lustre/bahamut/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac
  • Outfolder: /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/summary/
  • Pipeline started at: (09-22 08:02:59) elapsed: 16.0 TIME

Version log:

  • Python version: 3.7.4
  • Pypiper dir: /sfs/qumulo/qhome/jps3dp/.local/lib/python3.7/site-packages/pypiper
  • Pypiper version: 0.12.1
  • Pipeline dir: /sfs/lustre/bahamut/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/pipelines
  • Pipeline version: 0.0.2
  • Pipeline hash: ee6500ecf6fdc9cf3b1890635d7ee92206ddc58b
  • Pipeline branch: * master
  • Pipeline date: 2020-09-21 10:57:52 -0400
  • Pipeline diff: 2 files changed, 9 insertions(+), 9 deletions(-)

Arguments passed to pipeline:

  • config_file: /sfs/lustre/bahamut/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/tutorial/tutorial.yaml
  • cores: 1
  • dirty: False
  • force_follow: False
  • logdev: False
  • mem: 16000
  • name: PEPATAC_tutorial
  • new_start: False
  • output_parent: /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/
  • recover: False
  • results: /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline
  • silent: False
  • skip_consensus: False
  • skip_table: False
  • testmode: False
  • verbosity: None

Target to produce: /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/summary/PEPATAC_tutorial_libComplexity.pdf,/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/summary/PEPATAC_tutorial_*_consensusPeaks.narrowPea,/scratch/jps3dp/data/tmp/pepatac_tutorial/processed/summary/PEPATAC_tutorial_peaks_coverage.tsv

Rscript /scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/tools/PEPATAC_summarizer.R /sfs/lustre/bahamut/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/tutorial/tutorial.yaml /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/ /scratch/jps3dp/data/tmp/pepatac_tutorial/processed/results_pipeline (23066)

Loading config file: /sfs/lustre/bahamut/scratch/jps3dp/data/tmp/pepatac_tutorial/tools/pepatac/examples/tutorial/tutorial.yaml
Creating assets summary...
Summary (n=2): /scratch/jps3dp/data/tmp/pepatac_tutorial/processed//PEPATAC_tutorial_assets_summary.tsv
Creating summary plots...
1 of 2 library complexity files available.
INFO: Found real counts for tutorial1 - Total (M): 0.87693 Unique (M): 0.87693

Successfully produced project summary plots.

Calculating hg38 consensus peak set from 2 samples...
Consensus peak set: /scratch/jps3dp/data/tmp/pepatac_tutorial/processed//summary/PEPATAC_tutorial_hg38_consensusPeaks.narrowPeak

Warning message:
In PEPATACr::peakCounts(prj, argv$output, argv$results, assets) :
  Peak coverage files are not derived from a singular reference peak set.

Command completed. Elapsed time: 0:00:52. Running peak memory: 0.827GB.
PID: 23066; Command: Rscript; Return code: 0; Memory used: 0.827GB

Pipeline completed. Epilogue

  • Elapsed time (this run): 0:01:09
  • Total elapsed time (all runs): 0:00:52
  • Peak memory (this run): 0.8265 GB
  • Pipeline completed time: 2020-09-22 08:03:51