GDAC_clinicalDataPickerPipeline Execution Log 10:09 PM Mon Dec 10, '12

Running as user: cgaadm_deadline

GDAC_clinicalDataPicker1 stage2File file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataMerger/BRCA/2123453/0.GDAC_clinicalDataMerger.Finished/BRCA.clin.merged.txt
GDAC_clinicalDataPicker1 selectFile file:/xchip/cga/reference/tcga/clinical/2012_11_14/stage3_params_clin_brca.tsv
GDAC_clinicalDataPicker1 nodeColumn 1
GDAC_clinicalDataPicker1 outPrefix BRCA
Execution Times:
Submitted: 22:09:35 10-12-12
Completed:
Elapsed: 02 hrs 03 mins 53 secs

step 1. GDAC_clinicalDataPicker [id: 251827] 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/BRCA/2123453/0.GDAC_clinicalDataMerger.Finished/BRCA.clin.merged.txt
selectFile file:/xchip/cga/reference/tcga/clinical/2012_11_14/stage3_params_clin_brca.tsv
nodeColumn 1
outPrefix BRCA
Output Files:
 BRCA.clin.merged.picked.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 22:09:50 10-12-12
Completed: 23:19:03 10-12-12
Elapsed: 01 hrs 09 mins 12 secs

step 2. GDAC_clinicalDataPickerReport [id: 251828] Clinical data report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00330:50
picked BRCA.clin.merged.picked.txt
Output Files:
 paramStats.txt
 nozzle.html
 diagram_clinic.png
 tier1Data.txt
 report_tcga.html.RData
 report_private.html.RData
 report_private.html.html
 report_public.html.html
 report_tcga.html.html
 nozzle.RData
 report_public.html.RData
 tier1_clinical_variables.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 22:09:50 10-12-12
Completed: 00:13:28 11-12-12
Elapsed: 02 hrs 03 mins 37 secs