GDAC_MergeDataFilesPipeline Execution Log 4:57 PM Mon Jul 2, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.KIRC.2012_06_23__00_00_19.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues9221948262075713829.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues7824244140841583260.tsv
GDAC_MergeDataFiles2 output filename KIRC
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data
Execution Times:
Submitted: 16:57:04 02-07-12
Completed:
Elapsed: 00 hrs 00 mins 40 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 118484] 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.KIRC.2012_06_23__00_00_19.samplestamp.txt
annotationid transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data
sdrffilename
datapathsfile dependentsValues9221948262075713829.tsv
Output Files:
 dcc_archive.properties
 KIRC.merger.sdrf.txt
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 16:57:04 02-07-12
Completed: 16:57:23 02-07-12
Elapsed: 00 hrs 00 mins 18 secs

step 2. GDAC_MergeDataFiles [id: 118485] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues7824244140841583260.tsv
output filename KIRC
row_column column
num_headers 1
filetype transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data
Output Files:
 KIRC.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt
 stdout.txt
Execution Times:
Submitted: 16:57:04 02-07-12
Completed: 16:57:43 02-07-12
Elapsed: 00 hrs 00 mins 38 secs