GDAC_DataMergerPipeline 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 protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_DataMergerPipeline/GBM/1971140/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_DataMerger2 output GBM.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt
GDAC_DataMerger2 dataPaths file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_DataMergerPipeline/GBM/1971140/GDAC_DataMerger2.dataPaths.input.tsv
Execution Times:
Submitted: 08:21:12 04-11-12
Completed:
Elapsed: 00 hrs 23 mins 28 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 218780] 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 protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data
sdrfName
doNotCreateManifest
datapathsfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_DataMergerPipeline/GBM/1971140/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: 08:23:35 04-11-12
Completed: 08:33:57 04-11-12
Elapsed: 00 hrs 10 mins 22 secs

step 2. GDAC_DataMerger [id: 218781] Merge a list of files into a single file. Validate that all the files have the same columns and row names.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00481:4
output GBM.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt
dataPaths file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_DataMergerPipeline/GBM/1971140/GDAC_DataMerger2.dataPaths.input.tsv
Output Files:
 GBM.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt
 .lsf.out
Execution Times:
Submitted: 08:23:35 04-11-12
Completed: 08:44:37 04-11-12
Elapsed: 00 hrs 21 mins 02 secs