GDAC_MergeDataFilesPipeline Execution Log 4:51 PM Mon Jul 2, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.LAML.2012_06_23__00_00_19.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues7937449870152376999.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues8897438557524014431.tsv
GDAC_MergeDataFiles2 output filename LAML
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data.data
Execution Times:
Submitted: 16:51:17 02-07-12
Completed:
Elapsed: 00 hrs 01 mins 18 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 118411] 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.LAML.2012_06_23__00_00_19.samplestamp.txt
annotationid rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data
sdrffilename
datapathsfile dependentsValues7937449870152376999.tsv
Output Files:
 dcc_archive.properties
 .lsf.out
 LAML.merger.sdrf.txt
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 16:51:17 02-07-12
Completed: 16:51:43 02-07-12
Elapsed: 00 hrs 00 mins 25 secs

step 2. GDAC_MergeDataFiles [id: 118412] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues8897438557524014431.tsv
output filename LAML
row_column column
num_headers 1
filetype rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data.data
Output Files:
 LAML.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__exon_expression__data.data.txt
 stdout.txt
Execution Times:
Submitted: 16:51:18 02-07-12
Completed: 16:52:33 02-07-12
Elapsed: 00 hrs 01 mins 15 secs