GDAC_MergeDataFilesPipeline Execution Log 9:39 PM Fri Jul 13, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.STAD.2012_07_07__00_00_03.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues8272413869665551839.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues5770368312046510819.tsv
GDAC_MergeDataFiles2 output filename STAD
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data.data
Execution Times:
Submitted: 21:39:53 13-07-12
Completed:
Elapsed: 00 hrs 56 mins 16 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 129145] 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.STAD.2012_07_07__00_00_03.samplestamp.txt
annotationid rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data
sdrffilename
datapathsfile dependentsValues8272413869665551839.tsv
Output Files:
 STAD.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 21:39:53 13-07-12
Completed: 21:41:27 13-07-12
Elapsed: 00 hrs 01 mins 33 secs

step 2. GDAC_MergeDataFiles [id: 129146] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues5770368312046510819.tsv
output filename STAD
row_column column
num_headers 1
filetype rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data.data
Output Files:
 STAD.rnaseq__illuminaga_rnaseq__bcgsc_ca__Level_3__splice_junction_expression__data.data.txt
 stdout.txt
Execution Times:
Submitted: 21:39:53 13-07-12
Completed: 22:36:05 13-07-12
Elapsed: 00 hrs 56 mins 11 secs