GDAC_MergeDataFilesPipeline Execution Log 6:44 PM Fri Dec 21, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.COAD.2012_12_21__11_18_10.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-NORMALS/2169246/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COAD-NORMALS/2169246/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename COAD-NORMALS
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: 18:44:25 21-12-12
Completed:
Elapsed: 01 hrs 04 mins 11 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 268662] 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.2012_12_21__11_18_10.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-NORMALS/2169246/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 dcc_archive.properties
 COAD.merger.sdrf.txt
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:45:47 21-12-12
Completed: 19:10:13 21-12-12
Elapsed: 00 hrs 24 mins 26 secs

step 2. GDAC_MergeDataFiles [id: 268663] 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-NORMALS/2169246/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename COAD-NORMALS
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-NORMALS.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: 18:45:47 21-12-12
Completed: 19:48:34 21-12-12
Elapsed: 01 hrs 02 mins 47 secs