GDAC_MergeDataFilesPipeline Execution Log 8:21 AM Sun Nov 4, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.GBM.2012_10_24__11_21_08.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationids exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/1971146/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_MergeDataFiles2 inputfilelist filename file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/1971146/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
GDAC_MergeDataFiles2 output filename GBM
GDAC_MergeDataFiles2 row_column column
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data
Execution Times:
Submitted: 08:21:20 04-11-12
Completed:
Elapsed: 00 hrs 55 mins 53 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 218796] 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:00467:11
samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.GBM.2012_10_24__11_21_08.samplestamp.txt
annotationids exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/1971146/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 GBM.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 08:23:39 04-11-12
Completed: 08:33:45 04-11-12
Elapsed: 00 hrs 10 mins 06 secs

step 2. GDAC_MergeDataFiles [id: 218797] 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/GBM/1971146/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv
output filename GBM
row_column column
num_headers 1
filetype exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data
Output Files:
 GBM.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 08:23:39 04-11-12
Completed: 09:17:08 04-11-12
Elapsed: 00 hrs 53 mins 28 secs