GDAC_MergeDataFilesPipeline Execution Log 12:09 PM Tue Mar 12, '13

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.KIRC.2013_03_09__11_03_12.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIRC/2711593/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIRC/2711593/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename KIRC
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data
Execution Times:
Submitted: 12:09:29 12-03-13
Completed:
Elapsed: 01 hrs 10 mins 32 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 341047] 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:00467:12
samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.KIRC.2013_03_09__11_03_12.samplestamp.txt
annotationids methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIRC/2711593/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 dcc_archive.properties
 KIRC.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 12:11:10 12-03-13
Completed: 12:41:02 12-03-13
Elapsed: 00 hrs 29 mins 52 secs

step 2. GDAC_MergeDataFiles [id: 341048] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIRC/2711593/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename KIRC
row_column column
num_headers 1
filetype methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data
Output Files:
 KIRC.methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:11:10 12-03-13
Completed: 13:20:00 12-03-13
Elapsed: 01 hrs 08 mins 49 secs