GDAC_CnmfIntegratedPipeline Execution Log 7:41 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/HNSC-TP/2900594/0.GDAC_MethylationPreprocess.Finished/HNSC-TP.meth.for_clustering.filtered_data.txt
GDAC_TopgenesforCluster1 selectedgenes 4424
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/GDAC_MethylationPreprocess/HNSC-TP/2900594/0.GDAC_MethylationPreprocess.Finished/HNSC-TP.meth.for_clustering.filtered_data.txt
GDAC_CnmfReports4 report methylation
Execution Times:
Submitted: 19:41:26 08-04-13
Completed:
Elapsed: 06 hrs 43 mins 18 secs

step 1. GDAC_TopgenesforCluster [id: 373449] 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/HNSC-TP/2900594/0.GDAC_MethylationPreprocess.Finished/HNSC-TP.meth.for_clustering.filtered_data.txt
selectedgenes 4424
outputprefix outputprefix
Output Files:
 outputprefix.expclu.gct
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:41:26 08-04-13
Completed: 22:16:40 08-04-13
Elapsed: 02 hrs 35 mins 13 secs

step 2. GDAC_NmfConsensusClustering [id: 373450] 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
 cnmf.consensus.plot.k8.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:41:26 08-04-13
Completed: 01:57:45 09-04-13
Elapsed: 06 hrs 16 mins 18 secs

step 3. GDAC_CNMFselectcluster [id: 373451] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:39
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output HNSC-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/HNSC-TP/2900594/0.GDAC_MethylationPreprocess.Finished/HNSC-TP.meth.for_clustering.filtered_data.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 HNSC-TP.cormatrix.png
 HNSC-TP.bestclus.txt
 HNSC-TP.silfig.png
 HNSC-TP.subclassmarkers.txt
 HNSC-TP.selectmarker.txt
 HNSC-TP.geneheatmap.png
 HNSC-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:41:26 08-04-13
Completed: 02:23:52 09-04-13
Elapsed: 06 hrs 42 mins 25 secs

step 4. GDAC_CnmfReports [id: 373452]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
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 methylation
Output Files:
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:41:26 08-04-13
Completed: 02:24:43 09-04-13
Elapsed: 06 hrs 43 mins 16 secs