GDAC_CnmfIntegratedPipeline Execution Log 5:57 AM Wed Jun 12, '13

Running as user: cgaadm

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA-TP/3527686/BLCA-TP.meth.by_max_stddev.data.txt
GDAC_TopgenesforCluster1 selectedgenes 10677
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output BLCA-TP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA-TP/3527686/BLCA-TP.meth.by_max_stddev.data.txt
GDAC_CnmfReports4 report methylation
Execution Times:
Submitted: 05:57:54 12-06-13
Completed:
Elapsed: 03 hrs 51 mins 48 secs

step 1. GDAC_TopgenesforCluster [id: 421068] 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/GDAC_MethylationPreprocess/BLCA-TP/3527686/BLCA-TP.meth.by_max_stddev.data.txt
selectedgenes 10677
outputprefix outputprefix
Output Files:
 .lsf.out
 outputprefix.expclu.gct
 stdout.txt
Execution Times:
Submitted: 05:57:54 12-06-13
Completed: 07:50:48 12-06-13
Elapsed: 01 hrs 52 mins 53 secs

step 2. GDAC_NmfConsensusClustering [id: 421069] 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: 05:57:54 12-06-13
Completed: 09:04:32 12-06-13
Elapsed: 03 hrs 06 mins 37 secs

step 3. GDAC_CNMFselectcluster [id: 421070] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:45
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output BLCA-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA-TP/3527686/BLCA-TP.meth.by_max_stddev.data.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 BLCA-TP.silfig.png
 BLCA-TP.cormatrix.png
 BLCA-TP.bestclus.txt
 BLCA-TP.subclassmarkers.txt
 BLCA-TP.selectmarker.txt
 BLCA-TP.geneheatmap.png
 BLCA-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 05:57:54 12-06-13
Completed: 09:49:11 12-06-13
Elapsed: 03 hrs 51 mins 16 secs

step 4. GDAC_CnmfReports [id: 421071]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:32
kclus BLCA-TP.silfig.png
markers BLCA-TP.subclassmarkers.txt
bestclu BLCA-TP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix BLCA-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 BLCA-TP.selectmarker.txt
heatmap BLCA-TP.geneheatmap.png
heatmapall BLCA-TP.geneheatmaptopgenes.png
report methylation
Output Files:
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 05:57:54 12-06-13
Completed: 09:49:41 12-06-13
Elapsed: 03 hrs 51 mins 46 secs