GDAC_CnmfIntegratedPipeline Execution Log 11:40 PM Sun Apr 8, '12

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD/868404/0.mRNAseq_preprocessor.Finished/COADREAD.mRNAseq_RPKM_tmm_log2.txt
GDAC_TopgenesforCluster1 selectedgenes 1500
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output COADREAD
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD/868404/0.mRNAseq_preprocessor.Finished/COADREAD.mRNAseq_RPKM_tmm_log2.txt
GDAC_CnmfReports4 report mRNAseq
Execution Times:
Submitted: 23:40:07 08-04-12
Completed:
Elapsed: 00 hrs 13 mins 09 secs

step 1. GDAC_TopgenesforCluster [id: 74870] 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:00205:20
expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD/868404/0.mRNAseq_preprocessor.Finished/COADREAD.mRNAseq_RPKM_tmm_log2.txt
selectedgenes 1500
outputprefix outputprefix
Output Files:
 outputprefix.expclu.gct
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 23:40:07 08-04-12
Completed: 23:41:43 08-04-12
Elapsed: 00 hrs 01 mins 35 secs

step 2. GDAC_NmfConsensusClustering [id: 74871] 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:00379:38
expfile outputprefix.expclu.gct
k int 2
k final 8
outputprefix cnmf
Output Files:
 cnmf.normalized.gct
 cnmf.params.txt
 cnmf.consensus.plot.k2.png
 cnmf.consensus.all.k.plot.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.consensus.plot.k8.png
 cnmf.cophenetic.coefficient.txt
 cnmf.membership.txt
 cnmf.cophenetic.coefficient.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 23:40:07 08-04-12
Completed: 23:50:58 08-04-12
Elapsed: 00 hrs 10 mins 50 secs

step 3. GDAC_CNMFselectcluster [id: 74872] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:24
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output COADREAD
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD/868404/0.mRNAseq_preprocessor.Finished/COADREAD.mRNAseq_RPKM_tmm_log2.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 COADREAD.silfig.png
 COADREAD.cormatrix.png
 COADREAD.bestclus.txt
 COADREAD.subclassmarkers.txt
 COADREAD.seclectedSubclassmarkers.txt
 COADREAD.geneheatmap.png
 COADREAD.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 23:40:07 08-04-12
Completed: 23:52:45 08-04-12
Elapsed: 00 hrs 12 mins 37 secs

step 4. GDAC_CnmfReports [id: 74873]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:10
kclus COADREAD.silfig.png
markers COADREAD.subclassmarkers.txt
bestclu COADREAD.bestclus.txt
allcluster cnmf.membership.txt
cormatrix COADREAD.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 COADREAD.seclectedSubclassmarkers.txt
heatmap COADREAD.geneheatmap.png
heatmapall COADREAD.geneheatmaptopgenes.png
report mRNAseq
Output Files:
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 23:40:07 08-04-12
Completed: 23:53:15 08-04-12
Elapsed: 00 hrs 13 mins 07 secs