GDAC_DataMergerPipeline Execution Log 6:42 PM Fri Dec 21, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.COAD.2012_12_21__11_18_10.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/2169199/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/2169199/GDAC_DataMerger2.dataPaths.input.tsv
Execution Times:
Submitted: 18:42:37 21-12-12
Completed:
Elapsed: 00 hrs 59 mins 22 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 268554] 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.2012_12_21__11_18_10.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/2169199/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv
Output Files:
 COAD.merger.sdrf.txt
 dcc_archive.properties
 dcc_archive_manifest.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:45:03 21-12-12
Completed: 19:07:29 21-12-12
Elapsed: 00 hrs 22 mins 26 secs

step 2. GDAC_DataMerger [id: 268555] 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/2169199/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: 18:45:03 21-12-12
Completed: 19:41:59 21-12-12
Elapsed: 00 hrs 56 mins 56 secs