GDAC_MergeDataFilesPipeline Execution Log 7:08 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 mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues875008993019440049.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues6505630986431094653.tsv
GDAC_MergeDataFiles2 output filename UCEC
GDAC_MergeDataFiles2 row_column row
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data.data
Execution Times:
Submitted: 19:08:19 02-07-12
Completed:
Elapsed: 00 hrs 02 mins 36 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 118993] 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 mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data
sdrffilename
datapathsfile dependentsValues875008993019440049.tsv
Output Files:
 UCEC.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 19:08:19 02-07-12
Completed: 19:09:37 02-07-12
Elapsed: 00 hrs 01 mins 17 secs

step 2. GDAC_MergeDataFiles [id: 118994] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues6505630986431094653.tsv
output filename UCEC
row_column row
num_headers 1
filetype mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data.data
Output Files:
 UCEC.mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data.data.txt
 stdout.txt
Execution Times:
Submitted: 19:08:19 02-07-12
Completed: 19:10:53 02-07-12
Elapsed: 00 hrs 02 mins 33 secs