GDAC_MergeDataFilesPipeline Execution Log 7:10 PM Mon Jul 2, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.UCEC.2012_06_23__00_00_19.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues7032964290542718939.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues4385486891367469136.tsv
GDAC_MergeDataFiles2 output filename UCEC
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data.data
Execution Times:
Submitted: 19:10:19 02-07-12
Completed:
Elapsed: 00 hrs 39 mins 42 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 119015] 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:00467:9
samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.UCEC.2012_06_23__00_00_19.samplestamp.txt
annotationid rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data
sdrffilename
datapathsfile dependentsValues7032964290542718939.tsv
Output Files:
 UCEC.merger.sdrf.txt
 dcc_archive.properties
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:10:19 02-07-12
Completed: 19:12:34 02-07-12
Elapsed: 00 hrs 02 mins 14 secs

step 2. GDAC_MergeDataFiles [id: 119016] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues4385486891367469136.tsv
output filename UCEC
row_column column
num_headers 1
filetype rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data.data
Output Files:
 UCEC.rnaseq__illuminaga_rnaseq__unc_edu__Level_3__exon_expression__data.data.txt
 stdout.txt
Execution Times:
Submitted: 19:10:19 02-07-12
Completed: 19:50:00 02-07-12
Elapsed: 00 hrs 39 mins 40 secs