GDAC_CnmfIntegratedPipeline Execution Log 11:58 PM Thu Apr 4, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/PRAD-TP/2861220/0.CN_preprocess.Finished/PRAD-TP.cn_focal_gistic.txt
GDAC_TopgenesforCluster1 selectedgenes ALL
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/CN_preprocess/PRAD-TP/2861220/0.CN_preprocess.Finished/PRAD-TP.cn_focal_gistic.txt
GDAC_CnmfReports4 report nmfCN
Execution Times:
Submitted: 23:58:26 04-04-13
Completed:
Elapsed: 00 hrs 08 mins 06 secs

step 1. GDAC_TopgenesforCluster [id: 363993] 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:00205:36
expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/PRAD-TP/2861220/0.CN_preprocess.Finished/PRAD-TP.cn_focal_gistic.txt
selectedgenes ALL
outputprefix outputprefix
Output Files:
 .lsf.out
 outputprefix.expclu.gct
 stdout.txt
Execution Times:
Submitted: 23:58:26 04-04-13
Completed: 23:59:55 04-04-13
Elapsed: 00 hrs 01 mins 29 secs

step 2. GDAC_NmfConsensusClustering [id: 363994] 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: 23:58:26 04-04-13
Completed: 00:04:54 05-04-13
Elapsed: 00 hrs 06 mins 27 secs

step 3. GDAC_CNMFselectcluster [id: 363995] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:41
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output PRAD-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/PRAD-TP/2861220/0.CN_preprocess.Finished/PRAD-TP.cn_focal_gistic.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 PRAD-TP.bestclus.txt
 PRAD-TP.geneheatmap.png
 PRAD-TP.subclassmarkers.txt
 PRAD-TP.cormatrix.png
 PRAD-TP.selectmarker.txt
 PRAD-TP.silfig.png
 PRAD-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 23:58:26 04-04-13
Completed: 00:06:04 05-04-13
Elapsed: 00 hrs 07 mins 38 secs

step 4. GDAC_CnmfReports [id: 363996]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:24
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 nmfCN
Output Files:
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 23:58:26 04-04-13
Completed: 00:06:31 05-04-13
Elapsed: 00 hrs 08 mins 04 secs