Pipeline run code and environment:
- Command:
/scratch/jps3dp/tools/databio//peppro/pipelines/peppro_collator.py --config /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml -O /project/shefflab/processed//peppro/paper/6.11.2020 -P 1 -M 6000 -n PEPPRO -r /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline
- Compute host: udc-ba34-36
- Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
- Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/summary/
- Pipeline started at: (06-15 13:09:28) elapsed: 14.0 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: 0.0.3
- 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:
config_file
:/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml
cores
:1
dirty
:False
force_follow
:False
logdev
:False
mem
:6000
name
:PEPPRO
new_start
:False
output_parent
:/project/shefflab/processed//peppro/paper/6.11.2020
recover
:False
results
:/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline
silent
:False
testmode
:False
verbosity
:None
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO_libComplexity.pdf
,/project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO_countData.csv
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO_summarizer.R /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml /project/shefflab/processed//peppro/paper/6.11.2020 /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline
(124768)Loading config file: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml Creating assets summary... Summary (n=47): /project/shefflab/processed//peppro/paper/6.11.2020/PEPPRO_assets_summary.tsv 17 of 47 library complexity files available. Processing Jurkat_ChRO-seq_1 Processing Jurkat_ChRO-seq_2 Processing HEK_PRO-seq Processing HEK_ARF_PRO-seq Processing H9_treated_PRO-seq_1 Processing H9_treated_PRO-seq_2 Processing H9_treated_PRO-seq_3 Processing H9_PRO-seq_10 Processing H9_PRO-seq_20 Processing H9_PRO-seq_30 Processing H9_PRO-seq_40 Processing H9_PRO-seq_50 Processing H9_PRO-seq_60 Processing H9_PRO-seq_70 Processing H9_PRO-seq_80 Processing H9_PRO-seq_90 Processing H9_PRO-seq_100 INFO: Found real counts for Jurkat_ChRO-seq_1 - Total (M): 21.334642 Unique (M): 13.139331 INFO: Found real counts for Jurkat_ChRO-seq_2 - Total (M): 33.989659 Unique (M): 30.4684 INFO: Found real counts for HEK_PRO-seq - Total (M): 15.183469 Unique (M): 14.923343 INFO: Found real counts for HEK_ARF_PRO-seq - Total (M): 10.869678 Unique (M): 10.681803 INFO: Found real counts for H9_treated_PRO-seq_1 - Total (M): 19.73867 Unique (M): 18.664481 INFO: Found real counts for H9_treated_PRO-seq_2 - Total (M): 20.247016 Unique (M): 19.595024 INFO: Found real counts for H9_treated_PRO-seq_3 - Total (M): 22.825749 Unique (M): 20.168929 INFO: Found real counts for H9_PRO-seq_10 - Total (M): 1.945718 Unique (M): 1.966383 INFO: Found real counts for H9_PRO-seq_20 - Total (M): 3.896875 Unique (M): 3.908887 INFO: Found real counts for H9_PRO-seq_30 - Total (M): 5.844297 Unique (M): 5.818689 INFO: Found real counts for H9_PRO-seq_40 - Total (M): 7.79292 Unique (M): 7.703559 INFO: Found real counts for H9_PRO-seq_50 - Total (M): 9.741802 Unique (M): 9.562095 INFO: Found real counts for H9_PRO-seq_60 - Total (M): 11.690255 Unique (M): 11.393512 INFO: Found real counts for H9_PRO-seq_70 - Total (M): 13.641283 Unique (M): 13.202733 INFO: Found real counts for H9_PRO-seq_80 - Total (M): 15.588108 Unique (M): 14.983475 INFO: Found real counts for H9_PRO-seq_90 - Total (M): 17.534903 Unique (M): 16.739307 INFO: Found real counts for H9_PRO-seq_100 - Total (M): 19.4822 Unique (M): 18.471612
43 of 47 gene counts files available Counts table: /project/shefflab/processed//peppro/paper/6.11.2020/summary/PEPPRO_countData.csv
Command completed. Elapsed time: 0:00:45. Running peak memory: 0.526GB.
PID: 124768; Command: Rscript; Return code: 0; Memory used: 0.526GB
Pipeline completed. Epilogue
- Elapsed time (this run): 0:00:59
- Total elapsed time (all runs): 0:00:45
- Peak memory (this run): 0.5263 GB
- Pipeline completed time: 2020-06-15 13:10:13
Pipeline run code and environment:
- Command:
/scratch/jps3dp/tools/databio//peppro/pipelines/peppro_collator.py --config /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml -O /project/shefflab/processed//peppro/paper/6.11.2020 -P 1 -M 6000 -n PEPPRO -r /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline
- Compute host: udc-ba34-36
- Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
- Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/summary/
- Pipeline started at: (06-16 09:04:50) elapsed: 31.0 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: 0.0.3
- 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:
config_file
:/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml
cores
:1
dirty
:False
force_follow
:False
logdev
:False
mem
:6000
name
:PEPPRO
new_start
:False
output_parent
:/project/shefflab/processed//peppro/paper/6.11.2020
recover
:False
results
:/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline
silent
:False
testmode
:False
verbosity
:None
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO_libComplexity.pdf
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO_countData.csv
Pipeline completed. Epilogue
- Elapsed time (this run): 0:00:31
- Total elapsed time (all runs): 0:00:45
- Peak memory (this run): 0 GB
- Pipeline completed time: 2020-06-16 09:04:50 Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO collator_completed.flag'
Pipeline run code and environment:
- Command:
/scratch/jps3dp/tools/databio//peppro/pipelines/peppro_collator.py --config /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml -O /project/shefflab/processed//peppro/paper/6.11.2020 -P 1 -M 6000 -n PEPPRO -r /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline --new-start
- Compute host: udc-ba34-36
- Working dir: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc
- Outfolder: /project/shefflab/processed/peppro/paper/6.11.2020/summary/
- Pipeline started at: (06-16 09:05:10) elapsed: 0.0 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: 0.0.3
- 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:
config_file
:/sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml
cores
:1
dirty
:False
force_follow
:False
logdev
:False
mem
:6000
name
:PEPPRO
new_start
:True
output_parent
:/project/shefflab/processed//peppro/paper/6.11.2020
recover
:False
results
:/project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline
silent
:False
testmode
:False
verbosity
:None
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO_libComplexity.pdf
Target exists: /project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO_countData.csv
New start mode; run anyway.
Target to produce: /project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO_libComplexity.pdf
,/project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO_countData.csv
Rscript /scratch/jps3dp/tools/databio//peppro/tools/PEPPRO_summarizer.R /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml /project/shefflab/processed//peppro/paper/6.11.2020 /project/shefflab/processed//peppro/paper/6.11.2020/results_pipeline --new-start
(132188)Loading config file: /sfs/lustre/bahamut/scratch/jps3dp/tools/databio/ppqc/peppro_paper_rerun.yaml Creating assets summary... Summary (n=47): /project/shefflab/processed//peppro/paper/6.11.2020/PEPPRO_assets_summary.tsv 20 of 47 library complexity files available. Processing Jurkat_ChRO-seq_1 Processing Jurkat_ChRO-seq_2 Processing HEK_PRO-seq Processing HEK_ARF_PRO-seq Processing H9_PRO-seq_1 Processing H9_PRO-seq_2 Processing H9_PRO-seq_3 Processing H9_treated_PRO-seq_1 Processing H9_treated_PRO-seq_2 Processing H9_treated_PRO-seq_3 Processing H9_PRO-seq_10 Processing H9_PRO-seq_20 Processing H9_PRO-seq_30 Processing H9_PRO-seq_40 Processing H9_PRO-seq_50 Processing H9_PRO-seq_60 Processing H9_PRO-seq_70 Processing H9_PRO-seq_80 Processing H9_PRO-seq_90 Processing H9_PRO-seq_100 INFO: Found real counts for Jurkat_ChRO-seq_1 - Total (M): 21.334642 Unique (M): 13.139331 INFO: Found real counts for Jurkat_ChRO-seq_2 - Total (M): 33.989659 Unique (M): 30.4684 INFO: Found real counts for HEK_PRO-seq - Total (M): 15.183469 Unique (M): 14.923343 INFO: Found real counts for HEK_ARF_PRO-seq - Total (M): 10.869678 Unique (M): 10.681803 INFO: Found real counts for H9_PRO-seq_1 - Total (M): 21.966708 Unique (M): 20.33023 INFO: Found real counts for H9_PRO-seq_2 - Total (M): 19.4822 Unique (M): 18.471612 INFO: Found real counts for H9_PRO-seq_3 - Total (M): 19.481041 Unique (M): 19.005606 INFO: Found real counts for H9_treated_PRO-seq_1 - Total (M): 19.73867 Unique (M): 18.664481 INFO: Found real counts for H9_treated_PRO-seq_2 - Total (M): 20.247016 Unique (M): 19.595024 INFO: Found real counts for H9_treated_PRO-seq_3 - Total (M): 22.825749 Unique (M): 20.168929 INFO: Found real counts for H9_PRO-seq_10 - Total (M): 1.945718 Unique (M): 1.966383 INFO: Found real counts for H9_PRO-seq_20 - Total (M): 3.896875 Unique (M): 3.908887 INFO: Found real counts for H9_PRO-seq_30 - Total (M): 5.844297 Unique (M): 5.818689 INFO: Found real counts for H9_PRO-seq_40 - Total (M): 7.79292 Unique (M): 7.703559 INFO: Found real counts for H9_PRO-seq_50 - Total (M): 9.741802 Unique (M): 9.562095 INFO: Found real counts for H9_PRO-seq_60 - Total (M): 11.690255 Unique (M): 11.393512 INFO: Found real counts for H9_PRO-seq_70 - Total (M): 13.641283 Unique (M): 13.202733 INFO: Found real counts for H9_PRO-seq_80 - Total (M): 15.588108 Unique (M): 14.983475 INFO: Found real counts for H9_PRO-seq_90 - Total (M): 17.534903 Unique (M): 16.739307 INFO: Found real counts for H9_PRO-seq_100 - Total (M): 19.4822 Unique (M): 18.471612
47 of 47 gene counts files available Counts table: /project/shefflab/processed//peppro/paper/6.11.2020/summary/PEPPRO_countData.csv
Command completed. Elapsed time: 0:00:48. Running peak memory: 0.567GB.
PID: 132188; Command: Rscript; Return code: 0; Memory used: 0.567GB
Pipeline completed. Epilogue
- Elapsed time (this run): 0:00:48
- Total elapsed time (all runs): 0:00:48
- Peak memory (this run): 0.5671 GB
- Pipeline completed time: 2020-06-16 09:05:58 Removed existing flag: '/project/shefflab/processed/peppro/paper/6.11.2020/summary/PEPPRO collator_completed.flag'