GDAC_MergeDataFilesPipeline Execution Log 10:23 AM Mon Apr 8, '13

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.BLCA.2013_04_06__17_54_05.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BLCA/2895054/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BLCA/2895054/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename BLCA
GDAC_MergeDataFiles2 row_column row
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg
Execution Times:
Submitted: 10:23:20 08-04-13
Completed:
Elapsed: 00 hrs 06 mins 02 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 366538] 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.BLCA.2013_04_06__17_54_05.samplestamp.txt
annotationids cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BLCA/2895054/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 dcc_archive.properties
 BLCA.merger.sdrf.txt
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:23:20 08-04-13
Completed: 10:25:11 08-04-13
Elapsed: 00 hrs 01 mins 51 secs

step 2. GDAC_MergeDataFiles [id: 366539] 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/BLCA/2895054/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename BLCA
row_column row
num_headers 1
filetype cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg
Output Files:
 BLCA.cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:23:20 08-04-13
Completed: 10:29:21 08-04-13
Elapsed: 00 hrs 06 mins 00 secs