GDAC_clinicalDataPickerPipeline Execution Log 1:49 PM Tue Mar 12, '13

Running as user: cgaadm_deadline

GDAC_clinicalDataPicker1 stage2File file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataMerger/LUAD/2711896/0.GDAC_clinicalDataMerger.Finished/LUAD.clin.merged.txt
GDAC_clinicalDataPicker1 selectFile file:/xchip/cga/reference/tcga/clinical/2013_02_21/stage3_params_clin_luad.tsv
GDAC_clinicalDataPicker1 nodeColumn 1
GDAC_clinicalDataPicker1 outPrefix LUAD
Execution Times:
Submitted: 13:49:40 12-03-13
Completed:
Elapsed: 01 hrs 12 mins 52 secs

step 1. GDAC_clinicalDataPicker [id: 344787] 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/LUAD/2711896/0.GDAC_clinicalDataMerger.Finished/LUAD.clin.merged.txt
selectFile file:/xchip/cga/reference/tcga/clinical/2013_02_21/stage3_params_clin_luad.tsv
nodeColumn 1
outPrefix LUAD
Output Files:
 LUAD.clin.merged.picked.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:49:40 12-03-13
Completed: 14:23:37 12-03-13
Elapsed: 00 hrs 33 mins 57 secs

step 2. GDAC_clinicalDataPickerReport [id: 344788] Clinical data report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00330:50
picked LUAD.clin.merged.picked.txt
Output Files:
 nozzle.html
 diagram_clinic.png
 tier1Data.txt
 nozzle.RData
 paramStats.txt
 report_public.html.RData
 tier1_clinical_variables.txt
 report_tcga.html.RData
 report_private.html.RData
 report_private.html.html
 report_public.html.html
 report_tcga.html.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:49:40 12-03-13
Completed: 15:02:31 12-03-13
Elapsed: 01 hrs 12 mins 50 secs