GDAC_CnmfIntegratedPipeline Execution Log 12:42 AM Tue Apr 9, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/KIRP-TP/2904050/0.GDAC_MethylationPreprocess.Finished/KIRP-TP.meth.for_clustering.filtered_data.txt
GDAC_TopgenesforCluster1 selectedgenes 7742
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output KIRP-TP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/KIRP-TP/2904050/0.GDAC_MethylationPreprocess.Finished/KIRP-TP.meth.for_clustering.filtered_data.txt
GDAC_CnmfReports4 report methylation
Execution Times:
Submitted: 00:42:51 09-04-13
Completed:
Elapsed: 03 hrs 10 mins 13 secs

step 1. GDAC_TopgenesforCluster [id: 374296] 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/KIRP-TP/2904050/0.GDAC_MethylationPreprocess.Finished/KIRP-TP.meth.for_clustering.filtered_data.txt
selectedgenes 7742
outputprefix outputprefix
Output Files:
 .lsf.out
 outputprefix.expclu.gct
 stdout.txt
Execution Times:
Submitted: 00:42:51 09-04-13
Completed: 01:36:48 09-04-13
Elapsed: 00 hrs 53 mins 56 secs

step 2. GDAC_NmfConsensusClustering [id: 374297] 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.png
 cnmf.consensus.plot.k8.png
 cnmf.cophenetic.coefficient.txt
 cnmf.membership.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 00:42:51 09-04-13
Completed: 02:37:50 09-04-13
Elapsed: 01 hrs 54 mins 58 secs

step 3. GDAC_CNMFselectcluster [id: 374298] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:39
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output KIRP-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/KIRP-TP/2904050/0.GDAC_MethylationPreprocess.Finished/KIRP-TP.meth.for_clustering.filtered_data.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 KIRP-TP.cormatrix.png
 KIRP-TP.bestclus.txt
 KIRP-TP.silfig.png
 KIRP-TP.selectmarker.txt
 KIRP-TP.subclassmarkers.txt
 KIRP-TP.geneheatmap.png
 .lsf.out
 KIRP-TP.geneheatmaptopgenes.png
 stdout.txt
Execution Times:
Submitted: 00:42:51 09-04-13
Completed: 03:52:29 09-04-13
Elapsed: 03 hrs 09 mins 38 secs

step 4. GDAC_CnmfReports [id: 374299]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus KIRP-TP.silfig.png
markers KIRP-TP.subclassmarkers.txt
bestclu KIRP-TP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix KIRP-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 KIRP-TP.selectmarker.txt
heatmap KIRP-TP.geneheatmap.png
heatmapall KIRP-TP.geneheatmaptopgenes.png
report methylation
Output Files:
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 00:42:51 09-04-13
Completed: 03:53:03 09-04-13
Elapsed: 03 hrs 10 mins 11 secs