GDAC_CnmfIntegratedPipeline Execution Log 5:37 PM Fri Nov 9, '12

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA/2016696/0.GDAC_MethylationPreprocess.Finished/BLCA.meth.for_clustering.filtered_data.txt
GDAC_TopgenesforCluster1 selectedgenes 10059
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output BLCA
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA/2016696/0.GDAC_MethylationPreprocess.Finished/BLCA.meth.for_clustering.filtered_data.txt
GDAC_CnmfReports4 report methylation
Execution Times:
Submitted: 17:37:08 09-11-12
Completed:
Elapsed: 04 hrs 06 mins 09 secs

step 1. GDAC_TopgenesforCluster [id: 226574] 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:00205:35
expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA/2016696/0.GDAC_MethylationPreprocess.Finished/BLCA.meth.for_clustering.filtered_data.txt
selectedgenes 10059
outputprefix outputprefix
Output Files:
 .lsf.out
 outputprefix.expclu.gct
 stdout.txt
Execution Times:
Submitted: 17:37:08 09-11-12
Completed: 18:40:49 09-11-12
Elapsed: 01 hrs 03 mins 41 secs

step 2. GDAC_NmfConsensusClustering [id: 226575] 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: 17:37:08 09-11-12
Completed: 20:42:33 09-11-12
Elapsed: 03 hrs 05 mins 25 secs

step 3. GDAC_CNMFselectcluster [id: 226576] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:35
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output BLCA
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/BLCA/2016696/0.GDAC_MethylationPreprocess.Finished/BLCA.meth.for_clustering.filtered_data.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 BLCA.silfig.png
 BLCA.cormatrix.png
 BLCA.bestclus.txt
 BLCA.selectmarker.txt
 BLCA.subclassmarkers.txt
 BLCA.geneheatmap.png
 BLCA.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 17:37:08 09-11-12
Completed: 21:43:01 09-11-12
Elapsed: 04 hrs 05 mins 52 secs

step 4. GDAC_CnmfReports [id: 226577]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus BLCA.silfig.png
markers BLCA.subclassmarkers.txt
bestclu BLCA.bestclus.txt
allcluster cnmf.membership.txt
cormatrix BLCA.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.selectmarker.txt
heatmap BLCA.geneheatmap.png
heatmapall BLCA.geneheatmaptopgenes.png
report methylation
Output Files:
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 17:37:08 09-11-12
Completed: 21:43:16 09-11-12
Elapsed: 04 hrs 06 mins 07 secs