GDAC_MergeDataFilesPipeline Execution Log 12:06 PM Tue Mar 12, '13

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.GBM.2013_03_09__11_03_12.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/2711350/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/2711350/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename GBM
GDAC_MergeDataFiles2 row_column row
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg.seg
Execution Times:
Submitted: 12:06:02 12-03-13
Completed:
Elapsed: 01 hrs 01 mins 20 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 340330] 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.GBM.2013_03_09__11_03_12.samplestamp.txt
annotationids cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/2711350/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 GBM.merger.sdrf.txt
 dcc_archive.properties
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:07:37 12-03-13
Completed: 12:30:03 12-03-13
Elapsed: 00 hrs 22 mins 26 secs

step 2. GDAC_MergeDataFiles [id: 340331] 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/GBM/2711350/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename GBM
row_column row
num_headers 1
filetype cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg.seg
Output Files:
 GBM.cna__hg_cgh_244a__mskcc_org__Level_3__segmentation_data_computation__seg.seg.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:07:37 12-03-13
Completed: 13:07:20 12-03-13
Elapsed: 00 hrs 59 mins 43 secs