GDAC_MergeDataFilesPipeline Execution Log 7:42 PM Fri Dec 21, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.LIHC.2012_12_21__11_18_10.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LIHC-NORMALS/2170201/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LIHC-NORMALS/2170201/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename LIHC-NORMALS
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data.data
Execution Times:
Submitted: 19:42:17 21-12-12
Completed:
Elapsed: 01 hrs 10 mins 53 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 271187] 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.LIHC.2012_12_21__11_18_10.samplestamp.txt
annotationids rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LIHC-NORMALS/2170201/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 LIHC.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 19:42:25 21-12-12
Completed: 20:23:55 21-12-12
Elapsed: 00 hrs 41 mins 29 secs

step 2. GDAC_MergeDataFiles [id: 271188] 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/LIHC-NORMALS/2170201/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename LIHC-NORMALS
row_column column
num_headers 1
filetype rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data.data
Output Files:
 LIHC-NORMALS.rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data.data.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:42:25 21-12-12
Completed: 20:53:09 21-12-12
Elapsed: 01 hrs 10 mins 43 secs