GDAC_clinicalDataPickerPipeline Execution Log 10:14 PM Mon Dec 10, '12

Running as user: cgaadm_deadline

GDAC_clinicalDataPicker1 stage2File file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataMerger/LIHC/2124546/0.GDAC_clinicalDataMerger.Finished/LIHC.clin.merged.txt
GDAC_clinicalDataPicker1 selectFile file:/xchip/cga/reference/tcga/clinical/2012_11_14/stage3_params_clin_lihc.tsv
GDAC_clinicalDataPicker1 nodeColumn 1
GDAC_clinicalDataPicker1 outPrefix LIHC
Execution Times:
Submitted: 22:14:36 10-12-12
Completed:
Elapsed: 02 hrs 04 mins 03 secs

step 1. GDAC_clinicalDataPicker [id: 251929] 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/LIHC/2124546/0.GDAC_clinicalDataMerger.Finished/LIHC.clin.merged.txt
selectFile file:/xchip/cga/reference/tcga/clinical/2012_11_14/stage3_params_clin_lihc.tsv
nodeColumn 1
outPrefix LIHC
Output Files:
 LIHC.clin.merged.picked.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 22:14:46 10-12-12
Completed: 23:21:35 10-12-12
Elapsed: 01 hrs 06 mins 49 secs

step 2. GDAC_clinicalDataPickerReport [id: 251930] Clinical data report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00330:50
picked LIHC.clin.merged.picked.txt
Output Files:
 diagram_clinic.png
 tier1Data.txt
 nozzle.RData
 paramStats.txt
 tier1_clinical_variables.txt
 nozzle.html
 report_tcga.html.RData
 report_private.html.RData
 report_private.html.html
 report_public.html.html
 report_tcga.html.html
 .lsf.out
 report_public.html.RData
 stdout.txt
Execution Times:
Submitted: 22:14:46 10-12-12
Completed: 00:18:38 11-12-12
Elapsed: 02 hrs 03 mins 51 secs