GDAC_MergeDataFilesPipeline Execution Log 9:46 PM Fri Dec 21, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.OV.2012_12_21__11_18_10.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/2170568/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/2170568/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_loh__seg.seg
Execution Times:
Submitted: 21:46:47 21-12-12
Completed:
Elapsed: 00 hrs 31 mins 44 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 272186] 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_21__11_18_10.samplestamp.txt
annotationids snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/2170568/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: 21:47:22 21-12-12
Completed: 21:55:47 21-12-12
Elapsed: 00 hrs 08 mins 25 secs

step 2. GDAC_MergeDataFiles [id: 272187] 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/2170568/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename OV
row_column row
num_headers 1
filetype snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg.seg
Output Files:
 OV.snp__human1mduo__hudsonalpha_org__Level_3__segmented_loh__seg.seg.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 21:47:22 21-12-12
Completed: 22:18:26 21-12-12
Elapsed: 00 hrs 31 mins 04 secs