GDAC_MergeDataFilesPipeline Execution Log 4:40 PM Mon Apr 22, '13

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.UCEC.2013_04_21__00_00_28.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/UCEC/3025833/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/UCEC/3025833/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename UCEC
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: 16:40:19 22-04-13
Completed:
Elapsed: 13 hrs 24 mins 24 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 385467] 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.UCEC.2013_04_21__00_00_28.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/UCEC/3025833/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 UCEC.merger.sdrf.txt
 dcc_archive.properties
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 16:43:19 22-04-13
Completed: 17:22:38 22-04-13
Elapsed: 00 hrs 39 mins 19 secs

step 2. GDAC_MergeDataFiles [id: 385468] 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/UCEC/3025833/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename UCEC
row_column column
num_headers 1
filetype transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data
Output Files:
 UCEC.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 16:43:19 22-04-13
Completed: 06:04:41 23-04-13
Elapsed: 13 hrs 21 mins 21 secs