GDAC_CnmfIntegratedPipeline Execution Log 12:54 PM Thu Nov 8, '12

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/GBM/2008380/0.mRNAseq_preprocessor.Finished/GBM.uncv2.mRNAseq_RSEM_normalized_log2.txt
GDAC_TopgenesforCluster1 selectedgenes 1500
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 10
GDAC_CNMFselectcluster3 output GBM
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/GBM/2008380/0.mRNAseq_preprocessor.Finished/GBM.uncv2.mRNAseq_RSEM_normalized_log2.txt
GDAC_CnmfReports4 report mRNAseq
Execution Times:
Submitted: 12:54:50 08-11-12
Completed:
Elapsed: 00 hrs 25 mins 17 secs

step 1. GDAC_TopgenesforCluster [id: 222569] 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/GBM/2008380/0.mRNAseq_preprocessor.Finished/GBM.uncv2.mRNAseq_RSEM_normalized_log2.txt
selectedgenes 1500
outputprefix outputprefix
Output Files:
 outputprefix.expclu.gct
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:54:58 08-11-12
Completed: 12:57:18 08-11-12
Elapsed: 00 hrs 02 mins 19 secs

step 2. GDAC_NmfConsensusClustering [id: 222570] 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: 12:54:58 08-11-12
Completed: 13:13:54 08-11-12
Elapsed: 00 hrs 18 mins 55 secs

step 3. GDAC_CNMFselectcluster [id: 222571] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:33
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output GBM
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/GBM/2008380/0.mRNAseq_preprocessor.Finished/GBM.uncv2.mRNAseq_RSEM_normalized_log2.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 GBM.bestclus.txt
 GBM.silfig.png
 GBM.cormatrix.png
 GBM.subclassmarkers.txt
 GBM.selectmarker.txt
 GBM.geneheatmap.png
 GBM.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:54:58 08-11-12
Completed: 13:18:39 08-11-12
Elapsed: 00 hrs 23 mins 40 secs

step 4. GDAC_CnmfReports [id: 222572]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
kclus GBM.silfig.png
markers GBM.subclassmarkers.txt
bestclu GBM.bestclus.txt
allcluster cnmf.membership.txt
cormatrix GBM.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 GBM.selectmarker.txt
heatmap GBM.geneheatmap.png
heatmapall GBM.geneheatmaptopgenes.png
report mRNAseq
Output Files:
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:54:58 08-11-12
Completed: 13:20:06 08-11-12
Elapsed: 00 hrs 25 mins 07 secs