GDAC_CnmfIntegratedPipeline Execution Log 11:19 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/PANCAN12-TP/2901093/0.GDAC_mRNA_Preprocess_Median.Finished/PANCAN12-TP.medianexp.txt
GDAC_TopgenesforCluster1 selectedgenes 1500
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output PANCAN12-TP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/PANCAN12-TP/2901093/0.GDAC_mRNA_Preprocess_Median.Finished/PANCAN12-TP.medianexp.txt
GDAC_CnmfReports4 report mrna
Execution Times:
Submitted: 23:19:22 08-04-13
Completed:
Elapsed: 16 hrs 03 mins 40 secs

step 1. GDAC_TopgenesforCluster [id: 373708] This module can be used to selecte top genes with most variation, convert file to gct format, as well as imput missing value

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00205:35
expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/PANCAN12-TP/2901093/0.GDAC_mRNA_Preprocess_Median.Finished/PANCAN12-TP.medianexp.txt
selectedgenes 1500
outputprefix outputprefix
Output Files:
 outputprefix.expclu.gct
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 23:19:23 08-04-13
Completed: 00:36:29 09-04-13
Elapsed: 01 hrs 17 mins 06 secs

step 2. GDAC_NmfConsensusClustering [id: 373709] Non-negative Matrix Factorization (NMF) Consensus Clustering, http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=89

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00379:39
expfile outputprefix.expclu.gct
k int 2
k final 8
outputprefix cnmf
Output Files:
 cnmf.normalized.gct
 cnmf.params.txt
 cnmf.consensus.all.k.plot.png
 cnmf.consensus.plot.k2.png
 cnmf.consensus.plot.k3.png
 cnmf.consensus.plot.k4.png
 cnmf.consensus.plot.k5.png
 cnmf.consensus.plot.k6.png
 cnmf.consensus.plot.k7.png
 cnmf.cophenetic.coefficient.txt
 cnmf.membership.txt
 cnmf.cophenetic.coefficient.png
 .lsf.out
 cnmf.consensus.plot.k8.png
 stdout.txt
Execution Times:
Submitted: 23:19:23 08-04-13
Completed: 15:12:05 19-04-13
Elapsed: 15 hrs 52 mins 42 secs

step 3. GDAC_CNMFselectcluster [id: 373710] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:39
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output PANCAN12-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/PANCAN12-TP/2901093/0.GDAC_mRNA_Preprocess_Median.Finished/PANCAN12-TP.medianexp.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 PANCAN12-TP.silfig.png
 PANCAN12-TP.bestclus.txt
 PANCAN12-TP.cormatrix.png
 PANCAN12-TP.subclassmarkers.txt
 PANCAN12-TP.selectmarker.txt
 PANCAN12-TP.geneheatmap.png
 PANCAN12-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 23:19:23 08-04-13
Completed: 15:22:47 19-04-13
Elapsed: 16 hrs 03 mins 24 secs

step 4. GDAC_CnmfReports [id: 373711]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus PANCAN12-TP.silfig.png
markers PANCAN12-TP.subclassmarkers.txt
bestclu PANCAN12-TP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix PANCAN12-TP.cormatrix.png
file gif 2 cnmf.consensus.plot.k2.png
file gif 3 cnmf.consensus.plot.k3.png
file gif 4 cnmf.consensus.plot.k4.png
file gif 5 cnmf.consensus.plot.k5.png
file gif 6 cnmf.consensus.plot.k6.png
file gif 7 cnmf.consensus.plot.k7.png
file gif 8 cnmf.consensus.plot.k8.png
expdata outputprefix.expclu.gct
markersP PANCAN12-TP.selectmarker.txt
heatmap PANCAN12-TP.geneheatmap.png
heatmapall PANCAN12-TP.geneheatmaptopgenes.png
report mrna
Output Files:
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 23:19:23 08-04-13
Completed: 15:23:02 19-04-13
Elapsed: 16 hrs 03 mins 38 secs