### 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