GDAC_MergeDataFilesPipeline Execution Log 9:51 PM Fri Dec 21, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.PANCAN12.2012_12_21__11_18_10.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12/2170837/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12/2170837/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename PANCAN12
GDAC_MergeDataFiles2 row_column row
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg.seg
Execution Times:
Submitted: 21:51:47 21-12-12
Completed:
Elapsed: 01 hrs 07 mins 07 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 272893] 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.PANCAN12.2012_12_21__11_18_10.samplestamp.txt
annotationids snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12/2170837/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 PANCAN12.merger.sdrf.txt
 dcc_archive.properties
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 21:53:33 21-12-12
Completed: 22:16:46 21-12-12
Elapsed: 00 hrs 23 mins 12 secs

step 2. GDAC_MergeDataFiles [id: 272894] 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/PANCAN12/2170837/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename PANCAN12
row_column row
num_headers 1
filetype snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg.seg
Output Files:
 PANCAN12.snp__humanhap550__hudsonalpha_org__Level_3__segmented_cna__seg.seg.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 21:53:33 21-12-12
Completed: 22:58:52 21-12-12
Elapsed: 01 hrs 05 mins 19 secs