ParadigmPreprocessExpression1 broadFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUSC/1551625/2.GDAC_MergeDataFiles.Finished/LUSC.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt |
ParadigmPreprocessExpression1 exonFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUSC/1551697/2.GDAC_MergeDataFiles.Finished/LUSC.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt |
ParadigmPreprocessExpression1 uncFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUSC/1551609/2.GDAC_MergeDataFiles.Finished/LUSC.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt |
ParadigmPreprocess2 evidence prefix | LUSC |
ParadigmPrepare3 tolerance | 0.001 |
ParadigmPrepare3 nullBatches | 2 |
ParadigmPrepare3 minSampleFraction | 0.25 |
ParadigmPrepare3 minGeneFraction | 0.25 |
Paradigm4 tolerance | 0.001 |
Execution Times: | |
Submitted: | 18:11:11 01-08-12 |
Completed: | |
Elapsed: | 13 hrs 57 mins 23 secs |
step 1. ParadigmPreprocessExpression [id: 140901] Median center expression data before providing to PARADIGM.
urn:lsid:broadinstitute.org:cancer.genome.analysis:00420:9
broadFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUSC/1551625/2.GDAC_MergeDataFiles.Finished/LUSC.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt |
exonFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUSC/1551697/2.GDAC_MergeDataFiles.Finished/LUSC.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt |
uncFile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUSC/1551609/2.GDAC_MergeDataFiles.Finished/LUSC.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt |
broadNormalsFile | |
exonNormalsFile | |
uncNormalsFile |
Output Files: | |
RunR.sh | |
selectedExpressionFile.txt | |
normalizedExpression.txt | |
paradigmInputs.txt | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 18:11:11 01-08-12 |
Completed: | 18:13:26 01-08-12 |
Elapsed: | 00 hrs 02 mins 14 secs |
step 2. ParadigmPreprocess [id: 140902] Preprocessing module for broad data input to PARADIGM
urn:lsid:broadinstitute.org:cancer.genome.analysis:00366:9
evidence prefix | LUSC |
expression file | normalizedExpression.txt |
copynumber file | |
paradigm inputs | paradigmInputs.txt |
Output Files: | |
Evidence_LUSC.zip | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 18:11:11 01-08-12 |
Completed: | 18:52:01 01-08-12 |
Elapsed: | 00 hrs 40 mins 50 secs |
step 3. ParadigmPrepare [id: 140903] Gathers data files and prepares job lists for the iterative-scatter-gather PARADIGM run.
urn:lsid:broadinstitute.org:cancer.genome.analysis:00401:12
evidence | Evidence_LUSC.zip |
tolerance | 0.001 |
nullBatches | 2 |
pathwayZip | |
minSampleFraction | 0.25 |
minGeneFraction | 0.25 |
Output Files: | |
config.txt | |
configEM.txt | |
params0.txt | |
jobs.sh | |
templateEM.sh | |
clusterFiles.tar | |
.lsf.out |
Execution Times: | |
Submitted: | 18:11:11 01-08-12 |
Completed: | 19:01:08 01-08-12 |
Elapsed: | 00 hrs 49 mins 57 secs |
step 4. Paradigm [id: 140904] PARADIGM (PAthway Recognition Algorithm using Data Integration on Genomic Models)
urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21
tolerance | 0.001 |
clusterFilesTar | clusterFiles.tar |
configEM | configEM.txt |
templateEMScript | templateEM.sh |
config | config.txt |
jobsScript | jobs.sh |
paramsFile | params0.txt |
Output Files: | |
.lsf.out | |
stderr.txt | |
finalParams.txt | |
jobName.txt | |
inferredPathwayLevels.tab | |
mergeFiles.zip | |
finished | |
iterator.out.txt | |
jobSubmissions.txt | |
stdout.txt |
Execution Times: | |
Submitted: | 18:11:11 01-08-12 |
Completed: | 08:04:26 02-08-12 |
Elapsed: | 13 hrs 53 mins 15 secs |
step 5. ParadigmReportPreprocess [id: 140905] PARADIGM Report Preprocess
urn:lsid:broadinstitute.org:cancer.genome.analysis:00365:4
mergeFilesZip | mergeFiles.zip |
Output Files: | |
fontList.cache | |
resultPngs.zip | |
resultSummary.tab | |
resultTables.zip | |
pngToPathwayMap.txt | |
.lsf.out | |
stdout.txt |
Execution Times: | |
Submitted: | 18:11:11 01-08-12 |
Completed: | 08:06:58 02-08-12 |
Elapsed: | 13 hrs 55 mins 47 secs |
step 6. ParadigmReport [id: 140906] PARADIGM Report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00363:19
summaryTableFile | resultSummary.tab |
resultTablesZip | resultTables.zip |
resultPngsZip | resultPngs.zip |
pngToPathwayMapTxt | pngToPathwayMap.txt |
paradigmInputs | paradigmInputs.txt |
Execution Times: | |
Submitted: | 18:11:11 01-08-12 |
Completed: | 08:08:32 02-08-12 |
Elapsed: | 13 hrs 57 mins 20 secs |