GDAC_CnmfIntegratedPipeline Execution Log 12:08 AM Fri Apr 5, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/HNSC-TP/2861309/0.CN_preprocess.Finished/HNSC-TP.cn_focal_gistic.txt
GDAC_TopgenesforCluster1 selectedgenes ALL
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output HNSC-TP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/HNSC-TP/2861309/0.CN_preprocess.Finished/HNSC-TP.cn_focal_gistic.txt
GDAC_CnmfReports4 report nmfCN
Execution Times:
Submitted: 00:08:22 05-04-13
Completed:
Elapsed: 00 hrs 47 mins 47 secs

step 1. GDAC_TopgenesforCluster [id: 364099] 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/HNSC-TP/2861309/0.CN_preprocess.Finished/HNSC-TP.cn_focal_gistic.txt
selectedgenes ALL
outputprefix outputprefix
Output Files:
 .lsf.out
 outputprefix.expclu.gct
 stdout.txt
Execution Times:
Submitted: 00:08:26 05-04-13
Completed: 00:09:24 05-04-13
Elapsed: 00 hrs 00 mins 57 secs

step 2. GDAC_NmfConsensusClustering [id: 364100] 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: 00:08:26 05-04-13
Completed: 00:49:59 05-04-13
Elapsed: 00 hrs 41 mins 32 secs

step 3. GDAC_CNMFselectcluster [id: 364101] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:41
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output HNSC-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/HNSC-TP/2861309/0.CN_preprocess.Finished/HNSC-TP.cn_focal_gistic.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 HNSC-TP.silfig.png
 HNSC-TP.cormatrix.png
 HNSC-TP.subclassmarkers.txt
 HNSC-TP.bestclus.txt
 HNSC-TP.selectmarker.txt
 HNSC-TP.geneheatmap.png
 HNSC-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 00:08:26 05-04-13
Completed: 00:55:53 05-04-13
Elapsed: 00 hrs 47 mins 26 secs

step 4. GDAC_CnmfReports [id: 364102]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:24
kclus HNSC-TP.silfig.png
markers HNSC-TP.subclassmarkers.txt
bestclu HNSC-TP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix HNSC-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 HNSC-TP.selectmarker.txt
heatmap HNSC-TP.geneheatmap.png
heatmapall HNSC-TP.geneheatmaptopgenes.png
report nmfCN
Output Files:
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 00:08:26 05-04-13
Completed: 00:56:08 05-04-13
Elapsed: 00 hrs 47 mins 41 secs