GDAC_CnmfIntegratedPipeline Execution Log 1:15 PM Thu Jan 10, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/COAD-TP/2282948/0.CN_preprocess.Finished/COAD-TP.cn_focal_gistic.txt
GDAC_TopgenesforCluster1 selectedgenes ALL
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output COAD-TP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/COAD-TP/2282948/0.CN_preprocess.Finished/COAD-TP.cn_focal_gistic.txt
GDAC_CnmfReports4 report nmfCN
Execution Times:
Submitted: 13:15:19 10-01-13
Completed:
Elapsed: 01 hrs 08 mins 42 secs

step 1. GDAC_TopgenesforCluster [id: 285532] 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:00205:33
expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/COAD-TP/2282948/0.CN_preprocess.Finished/COAD-TP.cn_focal_gistic.txt
selectedgenes ALL
outputprefix outputprefix
Output Files:
 .lsf.out
 outputprefix.expclu.gct
 stdout.txt
Execution Times:
Submitted: 13:15:19 10-01-13
Completed: 13:16:05 10-01-13
Elapsed: 00 hrs 00 mins 45 secs

step 2. GDAC_NmfConsensusClustering [id: 285533] 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: 13:15:19 10-01-13
Completed: 14:22:17 10-01-13
Elapsed: 01 hrs 06 mins 57 secs

step 3. GDAC_CNMFselectcluster [id: 285534] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:34
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output COAD-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/COAD-TP/2282948/0.CN_preprocess.Finished/COAD-TP.cn_focal_gistic.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 COAD-TP.silfig.png
 COAD-TP.cormatrix.png
 COAD-TP.bestclus.txt
 COAD-TP.selectmarker.txt
 COAD-TP.subclassmarkers.txt
 COAD-TP.geneheatmap.png
 COAD-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:15:20 10-01-13
Completed: 14:23:14 10-01-13
Elapsed: 01 hrs 07 mins 54 secs

step 4. GDAC_CnmfReports [id: 285535]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus COAD-TP.silfig.png
markers COAD-TP.subclassmarkers.txt
bestclu COAD-TP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix COAD-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 COAD-TP.selectmarker.txt
heatmap COAD-TP.geneheatmap.png
heatmapall COAD-TP.geneheatmaptopgenes.png
report nmfCN
Output Files:
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:15:20 10-01-13
Completed: 14:24:00 10-01-13
Elapsed: 01 hrs 08 mins 40 secs