Mutsig_cluster_nozzle Execution Log 6:36 PM Wed Apr 17, '13

Running as user: cgaadm_deadline

mutsig2cluster_new1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/GBM-TP/2982741/GBM-TP.sample_sig_gene_table.txt
Correlate_Cluster_mutation_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/GBM-TP/2909397/1.GDAC_mergedClustering.Finished/GBM-TP.transferedmergedcluster.txt
Correlate_Cluster_mutation_onlysig2 filter cluster smaller than 3
Correlate_Cluster_mutation_onlysig2 output name GBM-TP
Correlate_Cluster_mutation_onlysig2 figure height 5
Correlate_Cluster_mutation_onlysig2 figure width 9
Correlate_Cluster_mutation_onlysig2 survival legend position OUT
Correlate_Cluster_mutation_onlysig2 pvalue cutoff 0.05
Correlate_Cluster_mutation_onlysig2 qvalue cutoff 0.25
Correlate_Cluster_mutation_onlysig2 make figure ONLYSIG
Correlate_Cluster_mutation_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 18:36:08 17-04-13
Completed:
Elapsed: 00 hrs 01 mins 14 secs

step 1. mutsig2cluster_new [id: 379285] Convert mutsig results to cluster files

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00336:4
sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/GBM-TP/2982741/GBM-TP.sample_sig_gene_table.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 GBM-TP.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:36:11 17-04-13
Completed: 18:36:36 17-04-13
Elapsed: 00 hrs 00 mins 25 secs

step 2. Correlate_Cluster_mutation_onlysig [id: 379286]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00503:3
cluster label file GBM-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/GBM-TP/2909397/1.GDAC_mergedClustering.Finished/GBM-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name GBM-TP
figure height 5
figure width 9
survival legend position OUT
pvalue cutoff 0.05
qvalue cutoff 0.25
make figure ONLYSIG
nozzle ver Nozzle.R1
options MUTSIG
report title
job description
Output Files:
 D3V5.png
 D3V8.pdf
 D3V8.png
 D3V5.pdf
 D3V7.pdf
 D3V7.png
 D4V3.pdf
 D4V1.pdf
 D4V5.png
 D4V2.pdf
 D4V4.png
 D4V5.pdf
 D4V2.png
 D4V1.png
 D4V4.pdf
 D4V3.png
 D6V5.png
 D6V1.pdf
 D6V1.png
 D6V5.pdf
 D41V5.png
 D41V1.pdf
 D41V2.png
 D41V2.pdf
 D41V1.png
 D41V4.png
 D41V5.pdf
 D41V4.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:36:11 17-04-13
Completed: 18:37:21 17-04-13
Elapsed: 00 hrs 01 mins 10 secs