GDAC_clinicalDataPickerPipeline Execution Log 6:43 AM Tue Feb 21, '12

Running as user: cgaadm_deadline

GDAC_clinicalDataPicker1 stage2File file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataMerger/BRCA/856086/0.GDAC_clinicalDataMerger.Finished/BRCA.clin.merged.txt
GDAC_clinicalDataPicker1 selectFile file:/xchip/cga/reference/clinical/2012_02_14/stage3_params_clin_brca.tsv
GDAC_clinicalDataPicker1 nodeColumn 1
GDAC_clinicalDataPicker1 outPrefix BRCA
Execution Times:
Submitted: 06:43:35 21-02-12
Completed:
Elapsed: 00 hrs 01 mins 21 secs

step 1. GDAC_clinicalDataPicker [id: 55807] 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/856086/0.GDAC_clinicalDataMerger.Finished/BRCA.clin.merged.txt
selectFile file:/xchip/cga/reference/clinical/2012_02_14/stage3_params_clin_brca.tsv
nodeColumn 1
outPrefix BRCA
Output Files:
 BRCA.clin.merged.picked.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 06:43:35 21-02-12
Completed: 06:44:09 21-02-12
Elapsed: 00 hrs 00 mins 33 secs

step 2. GDAC_clinicalDataPickerReport [id: 55808] Clinical data report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00330:43
picked BRCA.clin.merged.picked.txt
Output Files:
 diagram_clinic.png
 paramStats.txt
 tier1_clinical_variables.txt
 report_tcga.html_standalone.html
 report_public.html_standalone.html
 report_private.html_standalone.html
 tier1Data.txt
 report.html
 report_tcga.html.RData
 report.RData
 report_private.html.RData
 report_private.html.html
 report_standalone.html
 report_public.html.html
 report_tcga.html.html
 .lsf.out
 report_public.html.RData
 stdout.txt
Execution Times:
Submitted: 06:43:35 21-02-12
Completed: 06:44:55 21-02-12
Elapsed: 00 hrs 01 mins 20 secs