GDAC_MergeDataFilesPipeline Execution Log 12:14 PM Tue Mar 12, '13

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.LUAD.2013_03_09__11_03_12.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUAD/2711897/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUAD/2711897/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename LUAD
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data.data
Execution Times:
Submitted: 12:14:14 12-03-13
Completed:
Elapsed: 01 hrs 29 mins 27 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 341864] This module parses a samplestamp based on an input annotation id and creates an SDRF file as output.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00467:12
samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.LUAD.2013_03_09__11_03_12.samplestamp.txt
annotationids rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUAD/2711897/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 LUAD.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 12:20:28 12-03-13
Completed: 12:58:27 12-03-13
Elapsed: 00 hrs 37 mins 59 secs

step 2. GDAC_MergeDataFiles [id: 341865] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUAD/2711897/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename LUAD
row_column column
num_headers 1
filetype rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data.data
Output Files:
 LUAD.rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data.data.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:20:28 12-03-13
Completed: 13:43:40 12-03-13
Elapsed: 01 hrs 23 mins 11 secs