GDAC_DataMergerPipeline Execution Log 12:01 PM Tue Mar 12, '13

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.COAD.2013_03_09__11_03_12.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/COAD/2711155/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
GDAC_DataMerger2 output COAD.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/COAD/2711155/GDAC_DataMerger2.dataPaths.input.tsv
Execution Times:
Submitted: 12:01:06 12-03-13
Completed:
Elapsed: 00 hrs 43 mins 57 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 339760] 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.COAD.2013_03_09__11_03_12.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/COAD/2711155/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 dcc_archive.properties
 COAD.merger.sdrf.txt
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 12:02:10 12-03-13
Completed: 12:17:53 12-03-13
Elapsed: 00 hrs 15 mins 42 secs

step 2. GDAC_DataMerger [id: 339761] 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 COAD.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/COAD/2711155/GDAC_DataMerger2.dataPaths.input.tsv
Output Files:
 COAD.protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.data.txt
 .lsf.out
Execution Times:
Submitted: 12:02:10 12-03-13
Completed: 12:45:01 12-03-13
Elapsed: 00 hrs 42 mins 50 secs