GDAC_clinicalDataPickerPipeline Execution Log 12:38 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

GDAC_clinicalDataPicker1 stage2File file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataMerger/SKCM/2897828/0.GDAC_clinicalDataMerger.Finished/SKCM.clin.merged.txt
GDAC_clinicalDataPicker1 selectFile file:/xchip/cga/reference/tcga/clinical/2013_03_30/stage3_params_clin_skcm.tsv
GDAC_clinicalDataPicker1 nodeColumn 1
GDAC_clinicalDataPicker1 outPrefix SKCM
Execution Times:
Submitted: 12:38:49 08-04-13
Completed:
Elapsed: 06 hrs 12 mins 57 secs

step 1. GDAC_clinicalDataPicker [id: 372534] Picks out the clinical paramters of interest

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00312:26
stage2File file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataMerger/SKCM/2897828/0.GDAC_clinicalDataMerger.Finished/SKCM.clin.merged.txt
selectFile file:/xchip/cga/reference/tcga/clinical/2013_03_30/stage3_params_clin_skcm.tsv
nodeColumn 1
outPrefix SKCM
Output Files:
 SKCM.clin.merged.picked.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:38:49 08-04-13
Completed: 13:08:07 08-04-13
Elapsed: 00 hrs 29 mins 18 secs

step 2. GDAC_clinicalDataPickerReport [id: 372535] Clinical data report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00330:50
picked SKCM.clin.merged.picked.txt
Output Files:
 nozzle.html
 diagram_clinic.png
 tier1Data.txt
 report_tcga.html.RData
 report_public.html.html
 nozzle.RData
 paramStats.txt
 report_public.html.RData
 tier1_clinical_variables.txt
 report_private.html.RData
 report_private.html.html
 report_tcga.html.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:38:49 08-04-13
Completed: 18:51:45 08-04-13
Elapsed: 06 hrs 12 mins 55 secs