GDAC_CnmfIntegratedPipeline Execution Log 7:23 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/ESCA-TP/2900532/0.GDAC_MethylationPreprocess.Finished/ESCA-TP.meth.for_clustering.filtered_data.txt
GDAC_TopgenesforCluster1 selectedgenes 9036
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output ESCA-TP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/ESCA-TP/2900532/0.GDAC_MethylationPreprocess.Finished/ESCA-TP.meth.for_clustering.filtered_data.txt
GDAC_CnmfReports4 report methylation
Execution Times:
Submitted: 19:23:19 08-04-13
Completed:
Elapsed: 06 hrs 41 mins 13 secs

step 1. GDAC_TopgenesforCluster [id: 373357] 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/ESCA-TP/2900532/0.GDAC_MethylationPreprocess.Finished/ESCA-TP.meth.for_clustering.filtered_data.txt
selectedgenes 9036
outputprefix outputprefix
Output Files:
 outputprefix.expclu.gct
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:23:22 08-04-13
Completed: 22:14:04 08-04-13
Elapsed: 02 hrs 50 mins 41 secs

step 2. GDAC_NmfConsensusClustering [id: 373358] 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.plot.k4.png
 cnmf.consensus.plot.k2.png
 cnmf.consensus.all.k.plot.png
 cnmf.consensus.plot.k7.png
 cnmf.consensus.plot.k3.png
 cnmf.consensus.plot.k5.png
 cnmf.consensus.plot.k6.png
 cnmf.cophenetic.coefficient.txt
 cnmf.membership.txt
 cnmf.cophenetic.coefficient.png
 .lsf.out
 cnmf.consensus.plot.k8.png
 stdout.txt
Execution Times:
Submitted: 19:23:22 08-04-13
Completed: 00:56:40 09-04-13
Elapsed: 05 hrs 33 mins 17 secs

step 3. GDAC_CNMFselectcluster [id: 373359] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:39
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output ESCA-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/ESCA-TP/2900532/0.GDAC_MethylationPreprocess.Finished/ESCA-TP.meth.for_clustering.filtered_data.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 ESCA-TP.silfig.png
 ESCA-TP.cormatrix.png
 ESCA-TP.bestclus.txt
 ESCA-TP.subclassmarkers.txt
 ESCA-TP.selectmarker.txt
 ESCA-TP.geneheatmap.png
 ESCA-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:23:22 08-04-13
Completed: 02:03:54 09-04-13
Elapsed: 06 hrs 40 mins 31 secs

step 4. GDAC_CnmfReports [id: 373360]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus ESCA-TP.silfig.png
markers ESCA-TP.subclassmarkers.txt
bestclu ESCA-TP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix ESCA-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 ESCA-TP.selectmarker.txt
heatmap ESCA-TP.geneheatmap.png
heatmapall ESCA-TP.geneheatmaptopgenes.png
report methylation
Output Files:
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:23:22 08-04-13
Completed: 02:04:31 09-04-13
Elapsed: 06 hrs 41 mins 08 secs