GDAC_MergeDataFilesPipeline Execution Log 4:19 PM Mon Jul 2, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.GBM.2012_06_23__00_00_19.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues1835318223786396059.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues7295362134239819872.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__segmented_as_firma__data.data
Execution Times:
Submitted: 16:19:41 02-07-12
Completed:
Elapsed: 00 hrs 01 mins 34 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 118049] 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:00467:9
samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.GBM.2012_06_23__00_00_19.samplestamp.txt
annotationid exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data
sdrffilename
datapathsfile dependentsValues1835318223786396059.tsv
Output Files:
 GBM.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 16:19:42 02-07-12
Completed: 16:20:01 02-07-12
Elapsed: 00 hrs 00 mins 19 secs

step 2. GDAC_MergeDataFiles [id: 118050] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues7295362134239819872.tsv
output filename GBM
row_column column
num_headers 1
filetype exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data.data
Output Files:
 GBM.exon__huex_1_0_st_v2__lbl_gov__Level_3__segmented_as_firma__data.data.txt
 stdout.txt
Execution Times:
Submitted: 16:19:42 02-07-12
Completed: 16:21:15 02-07-12
Elapsed: 00 hrs 01 mins 33 secs