GDAC_CnmfIntegratedPipeline Execution Log 10:12 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/PRAD-TP/2901094/0.GDAC_MethylationPreprocess.Finished/PRAD-TP.meth.for_clustering.filtered_data.txt
GDAC_TopgenesforCluster1 selectedgenes 2769
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output PRAD-TP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/PRAD-TP/2901094/0.GDAC_MethylationPreprocess.Finished/PRAD-TP.meth.for_clustering.filtered_data.txt
GDAC_CnmfReports4 report methylation
Execution Times:
Submitted: 22:12:02 08-04-13
Completed:
Elapsed: 04 hrs 06 mins 50 secs

step 1. GDAC_TopgenesforCluster [id: 373483] 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_MethylationPreprocess/PRAD-TP/2901094/0.GDAC_MethylationPreprocess.Finished/PRAD-TP.meth.for_clustering.filtered_data.txt
selectedgenes 2769
outputprefix outputprefix
Output Files:
 .lsf.out
 outputprefix.expclu.gct
 stdout.txt
Execution Times:
Submitted: 22:12:03 08-04-13
Completed: 00:22:32 09-04-13
Elapsed: 02 hrs 10 mins 29 secs

step 2. GDAC_NmfConsensusClustering [id: 373484] 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: 22:12:03 08-04-13
Completed: 01:50:49 09-04-13
Elapsed: 03 hrs 38 mins 46 secs

step 3. GDAC_CNMFselectcluster [id: 373485] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:39
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output PRAD-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/PRAD-TP/2901094/0.GDAC_MethylationPreprocess.Finished/PRAD-TP.meth.for_clustering.filtered_data.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 PRAD-TP.bestclus.txt
 PRAD-TP.cormatrix.png
 PRAD-TP.silfig.png
 PRAD-TP.subclassmarkers.txt
 PRAD-TP.selectmarker.txt
 PRAD-TP.geneheatmap.png
 PRAD-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 22:12:03 08-04-13
Completed: 02:18:33 09-04-13
Elapsed: 04 hrs 06 mins 29 secs

step 4. GDAC_CnmfReports [id: 373486]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus PRAD-TP.silfig.png
markers PRAD-TP.subclassmarkers.txt
bestclu PRAD-TP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix PRAD-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 PRAD-TP.selectmarker.txt
heatmap PRAD-TP.geneheatmap.png
heatmapall PRAD-TP.geneheatmaptopgenes.png
report methylation
Output Files:
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 22:12:03 08-04-13
Completed: 02:18:50 09-04-13
Elapsed: 04 hrs 06 mins 47 secs