GDAC_MergeDataFilesPipeline Execution Log 6:12 PM Mon Dec 10, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.COADREAD.2012_12_06__00_00_32.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD-NORMALS/2123825/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD-NORMALS/2123825/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename COADREAD-NORMALS
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data
Execution Times:
Submitted: 18:12:33 10-12-12
Completed:
Elapsed: 01 hrs 26 mins 49 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 245684] 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.COADREAD.2012_12_06__00_00_32.samplestamp.txt
annotationids transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD-NORMALS/2123825/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 COADREAD.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 18:15:00 10-12-12
Completed: 18:45:46 10-12-12
Elapsed: 00 hrs 30 mins 45 secs

step 2. GDAC_MergeDataFiles [id: 245685] 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/COADREAD-NORMALS/2123825/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename COADREAD-NORMALS
row_column column
num_headers 1
filetype transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data
Output Files:
 COADREAD-NORMALS.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:15:00 10-12-12
Completed: 19:39:21 10-12-12
Elapsed: 01 hrs 24 mins 20 secs