GDAC_MergeDataFilesPipeline Execution Log 7:46 PM Mon Dec 10, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.OV.2012_12_06__00_00_32.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/2124947/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/2124947/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename OV
GDAC_MergeDataFiles2 row_column row
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg.seg
Execution Times:
Submitted: 19:46:54 10-12-12
Completed:
Elapsed: 02 hrs 07 mins 03 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 248601] 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.OV.2012_12_06__00_00_32.samplestamp.txt
annotationids snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/2124947/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 dcc_archive.properties
 OV.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 19:47:00 10-12-12
Completed: 20:56:45 10-12-12
Elapsed: 01 hrs 09 mins 45 secs

step 2. GDAC_MergeDataFiles [id: 248602] 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/OV/2124947/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename OV
row_column row
num_headers 1
filetype snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg.seg
Output Files:
 OV.snp__human1mduo__hudsonalpha_org__Level_3__segmented_cna__seg.seg.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:47:00 10-12-12
Completed: 21:53:56 10-12-12
Elapsed: 02 hrs 06 mins 55 secs