GDAC_CnmfIntegratedPipeline Execution Log 3:05 PM Thu May 2, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/LIHC-TP/3142820/0.CN_preprocess.Finished/LIHC-TP.cn_focal_gistic.txt
GDAC_TopgenesforCluster1 selectedgenes ALL
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output LIHC-TP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/LIHC-TP/3142820/0.CN_preprocess.Finished/LIHC-TP.cn_focal_gistic.txt
GDAC_CnmfReports4 report nmfCN
Execution Times:
Submitted: 15:05:47 02-05-13
Completed:
Elapsed: 00 hrs 03 mins 47 secs

step 1. GDAC_TopgenesforCluster [id: 396701] 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/LIHC-TP/3142820/0.CN_preprocess.Finished/LIHC-TP.cn_focal_gistic.txt
selectedgenes ALL
outputprefix outputprefix
Output Files:
 .lsf.out
 outputprefix.expclu.gct
 stdout.txt
Execution Times:
Submitted: 15:05:48 02-05-13
Completed: 15:06:37 02-05-13
Elapsed: 00 hrs 00 mins 49 secs

step 2. GDAC_NmfConsensusClustering [id: 396702] 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: 15:05:48 02-05-13
Completed: 15:08:13 02-05-13
Elapsed: 00 hrs 02 mins 25 secs

step 3. GDAC_CNMFselectcluster [id: 396703] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:41
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output LIHC-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/CN_preprocess/LIHC-TP/3142820/0.CN_preprocess.Finished/LIHC-TP.cn_focal_gistic.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 LIHC-TP.subclassmarkers.txt
 LIHC-TP.selectmarker.txt
 LIHC-TP.bestclus.txt
 LIHC-TP.cormatrix.png
 LIHC-TP.silfig.png
 LIHC-TP.geneheatmap.png
 LIHC-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:05:48 02-05-13
Completed: 15:09:03 02-05-13
Elapsed: 00 hrs 03 mins 15 secs

step 4. GDAC_CnmfReports [id: 396704]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:24
kclus LIHC-TP.silfig.png
markers LIHC-TP.subclassmarkers.txt
bestclu LIHC-TP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix LIHC-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 LIHC-TP.selectmarker.txt
heatmap LIHC-TP.geneheatmap.png
heatmapall LIHC-TP.geneheatmaptopgenes.png
report nmfCN
Output Files:
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 15:05:48 02-05-13
Completed: 15:09:34 02-05-13
Elapsed: 00 hrs 03 mins 45 secs