GDAC_CnmfIntegratedPipeline Execution Log 4:00 PM Thu Jan 10, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/2284143/0.mRNAseq_preprocessor.Finished/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
GDAC_TopgenesforCluster1 selectedgenes 1500
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 10
GDAC_CNMFselectcluster3 output THCA-TP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/2284143/0.mRNAseq_preprocessor.Finished/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
GDAC_CnmfReports4 report mRNAseq
Execution Times:
Submitted: 16:00:59 10-01-13
Completed:
Elapsed: 05 hrs 36 mins 20 secs

step 1. GDAC_TopgenesforCluster [id: 286416] 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:00205:33
expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/2284143/0.mRNAseq_preprocessor.Finished/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
selectedgenes 1500
outputprefix outputprefix
Output Files:
 outputprefix.expclu.gct
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 16:01:08 10-01-13
Completed: 16:05:09 10-01-13
Elapsed: 00 hrs 04 mins 00 secs

step 2. GDAC_NmfConsensusClustering [id: 286417] 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 10
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.consensus.plot.k8.png
 cnmf.consensus.plot.k9.png
 cnmf.cophenetic.coefficient.txt
 cnmf.membership.txt
 cnmf.cophenetic.coefficient.png
 .lsf.out
 cnmf.consensus.plot.k10.png
 stdout.txt
Execution Times:
Submitted: 16:01:08 10-01-13
Completed: 21:32:51 10-01-13
Elapsed: 05 hrs 31 mins 42 secs

step 3. GDAC_CNMFselectcluster [id: 286418] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:33
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output THCA-TP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/2284143/0.mRNAseq_preprocessor.Finished/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 THCA-TP.silfig.png
 THCA-TP.bestclus.txt
 THCA-TP.cormatrix.png
 THCA-TP.subclassmarkers.txt
 THCA-TP.selectmarker.txt
 THCA-TP.geneheatmap.png
 .lsf.out
 THCA-TP.geneheatmaptopgenes.png
 stdout.txt
Execution Times:
Submitted: 16:01:08 10-01-13
Completed: 21:36:47 10-01-13
Elapsed: 05 hrs 35 mins 39 secs

step 4. GDAC_CnmfReports [id: 286419]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus THCA-TP.silfig.png
markers THCA-TP.subclassmarkers.txt
bestclu THCA-TP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix THCA-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 THCA-TP.selectmarker.txt
heatmap THCA-TP.geneheatmap.png
heatmapall THCA-TP.geneheatmaptopgenes.png
report mRNAseq
Output Files:
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 16:01:08 10-01-13
Completed: 21:37:18 10-01-13
Elapsed: 05 hrs 36 mins 10 secs