GDAC_clinicalDataPickerPipeline Execution Log 1:46 PM Tue Mar 12, '13

Running as user: cgaadm_deadline

GDAC_clinicalDataPicker1 stage2File file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataMerger/COADREAD/2711228/0.GDAC_clinicalDataMerger.Finished/COADREAD.clin.merged.txt
GDAC_clinicalDataPicker1 selectFile file:/xchip/cga/reference/tcga/clinical/2013_02_21/stage3_params_clin_coadread.tsv
GDAC_clinicalDataPicker1 nodeColumn 1
GDAC_clinicalDataPicker1 outPrefix COADREAD
Execution Times:
Submitted: 13:46:08 12-03-13
Completed:
Elapsed: 01 hrs 13 mins 44 secs

step 1. GDAC_clinicalDataPicker [id: 344684] 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/COADREAD/2711228/0.GDAC_clinicalDataMerger.Finished/COADREAD.clin.merged.txt
selectFile file:/xchip/cga/reference/tcga/clinical/2013_02_21/stage3_params_clin_coadread.tsv
nodeColumn 1
outPrefix COADREAD
Output Files:
 COADREAD.clin.merged.picked.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:46:21 12-03-13
Completed: 14:22:09 12-03-13
Elapsed: 00 hrs 35 mins 48 secs

step 2. GDAC_clinicalDataPickerReport [id: 344685] Clinical data report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00330:50
picked COADREAD.clin.merged.picked.txt
Output Files:
 paramStats.txt
 diagram_clinic.png
 tier1_clinical_variables.txt
 tier1Data.txt
 nozzle.RData
 nozzle.html
 report_tcga.html.RData
 report_private.html.RData
 report_public.html.html
 report_tcga.html.html
 report_public.html.RData
 report_private.html.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:46:21 12-03-13
Completed: 14:59:52 12-03-13
Elapsed: 01 hrs 13 mins 31 secs