GDAC_CnmfIntegratedPipeline Execution Log 5:58 PM Wed Aug 1, '12

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt
GDAC_TopgenesforCluster1 selectedgenes 1500
GDAC_NmfConsensusClustering2 k int 2
GDAC_NmfConsensusClustering2 k final 8
GDAC_CNMFselectcluster3 output KIRP
GDAC_CNMFselectcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt
GDAC_CnmfReports4 report mrna
Execution Times:
Submitted: 17:58:06 01-08-12
Completed:
Elapsed: 00 hrs 32 mins 04 secs

step 1. GDAC_TopgenesforCluster [id: 140712] 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:00205:29
expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt
selectedgenes 1500
outputprefix outputprefix
Output Files:
 .lsf.out
 outputprefix.expclu.gct
 stdout.txt
Execution Times:
Submitted: 17:58:07 01-08-12
Completed: 17:59:29 01-08-12
Elapsed: 00 hrs 01 mins 22 secs

step 2. GDAC_NmfConsensusClustering [id: 140713] 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.cophenetic.coefficient.txt
 cnmf.consensus.plot.k2.png
 cnmf.consensus.all.k.plot.png
 cnmf.consensus.plot.k7.png
 cnmf.consensus.plot.k3.png
 cnmf.membership.txt
 cnmf.cophenetic.coefficient.png
 cnmf.consensus.plot.k5.png
 cnmf.consensus.plot.k8.png
 cnmf.consensus.plot.k6.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 17:58:07 01-08-12
Completed: 18:28:52 01-08-12
Elapsed: 00 hrs 30 mins 45 secs

step 3. GDAC_CNMFselectcluster [id: 140714] selecte best cluster

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:27
measure Pearson
inputexp outputprefix.expclu.gct
clumembership cnmf.membership.txt
output KIRP
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRP/1590232/0.GDAC_mRNA_Preprocess_Median.Finished/KIRP.medianexp.txt
cophenetic cnmf.cophenetic.coefficient.txt
Output Files:
 KIRP.cormatrix.png
 KIRP.silfig.png
 KIRP.bestclus.txt
 KIRP.geneheatmap.png
 KIRP.subclassmarkers.txt
 KIRP.selectedSubclassmarkers.txt
 KIRP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 17:58:07 01-08-12
Completed: 18:29:37 01-08-12
Elapsed: 00 hrs 31 mins 30 secs

step 4. GDAC_CnmfReports [id: 140715]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:19
kclus KIRP.silfig.png
markers KIRP.subclassmarkers.txt
bestclu KIRP.bestclus.txt
allcluster cnmf.membership.txt
cormatrix KIRP.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.selectedSubclassmarkers.txt
heatmap KIRP.geneheatmap.png
heatmapall KIRP.geneheatmaptopgenes.png
report mrna
Output Files:
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 17:58:07 01-08-12
Completed: 18:30:09 01-08-12
Elapsed: 00 hrs 32 mins 02 secs