GDAC_MergeDataFilesPipeline Execution Log 12:01 PM Tue Mar 12, '13

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.COAD.2013_03_09__11_03_12.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COAD/2711154/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COAD/2711154/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename COAD
GDAC_MergeDataFiles2 row_column row
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg
Execution Times:
Submitted: 12:01:05 12-03-13
Completed:
Elapsed: 00 hrs 46 mins 45 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 339756] 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.COAD.2013_03_09__11_03_12.samplestamp.txt
annotationids snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COAD/2711154/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 dcc_archive.properties
 COAD.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 12:02:10 12-03-13
Completed: 12:18:13 12-03-13
Elapsed: 00 hrs 16 mins 03 secs

step 2. GDAC_MergeDataFiles [id: 339758] 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/COAD/2711154/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename COAD
row_column row
num_headers 1
filetype snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg
Output Files:
 COAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:02:10 12-03-13
Completed: 12:47:49 12-03-13
Elapsed: 00 hrs 45 mins 39 secs