| 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 |
| ParadigmPreprocess2 copynumber file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/LUSC/1590406/1.GetReducedSegments.Finished/LUSC.RS.tsv |
| ParadigmPrepare3 tolerance | 0.001 |
| ParadigmPrepare3 nullBatches | 2 |
| ParadigmPrepare3 minSampleFraction | 0.01 |
| ParadigmPrepare3 minGeneFraction | 0.25 |
| Paradigm4 tolerance | 0.001 |
| Execution Times: | |
| Submitted: | 18:18:54 01-08-12 |
| Completed: | |
| Elapsed: | 07 hrs 34 mins 21 secs |
step 1. ParadigmPreprocessExpression [id: 140961] 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: | 18:18:54 01-08-12 |
| Completed: | 18:19:37 01-08-12 |
| Elapsed: | 00 hrs 00 mins 43 secs |
step 2. ParadigmPreprocess [id: 140962] 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 | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/LUSC/1590406/1.GetReducedSegments.Finished/LUSC.RS.tsv |
| paradigm inputs | paradigmInputs.txt |
| Output Files: | |
| Evidence_LUSC.zip | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 18:18:54 01-08-12 |
| Completed: | 18:54:20 01-08-12 |
| Elapsed: | 00 hrs 35 mins 26 secs |
step 3. ParadigmPrepare [id: 140963] 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 | 0.01 |
| minGeneFraction | 0.25 |
| Output Files: | |
| config.txt | |
| configEM.txt | |
| params0.txt | |
| jobs.sh | |
| templateEM.sh | |
| clusterFiles.tar | |
| .lsf.out | |
| Execution Times: | |
| Submitted: | 18:18:54 01-08-12 |
| Completed: | 19:10:35 01-08-12 |
| Elapsed: | 00 hrs 51 mins 41 secs |
step 4. Paradigm [id: 140964] 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: | 18:18:54 01-08-12 |
| Completed: | 01:48:59 02-08-12 |
| Elapsed: | 07 hrs 30 mins 04 secs |
step 5. ParadigmReportPreprocess [id: 140965] 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: | 18:18:54 01-08-12 |
| Completed: | 01:51:39 02-08-12 |
| Elapsed: | 07 hrs 32 mins 44 secs |
step 6. ParadigmReport [id: 140966] 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: | 18:18:54 01-08-12 |
| Completed: | 01:53:12 02-08-12 |
| Elapsed: | 07 hrs 34 mins 17 secs |