Mutsig_cluster_nozzle Execution Log 7:45 PM Thu May 2, '13

Running as user: cgaadm_deadline

mutsig2cluster_new1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LUAD-TP/2905496/LUAD-TP.sample_sig_gene_table.txt
Correlate_Cluster_mutation_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LUAD-TP/3145444/1.GDAC_mergedClustering.Finished/LUAD-TP.transferedmergedcluster.txt
Correlate_Cluster_mutation_onlysig2 filter cluster smaller than 3
Correlate_Cluster_mutation_onlysig2 output name LUAD-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: 19:45:18 02-05-13
Completed:
Elapsed: 00 hrs 03 mins 35 secs

step 1. mutsig2cluster_new [id: 397796] 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/LUAD-TP/2905496/LUAD-TP.sample_sig_gene_table.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 LUAD-TP.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:45:18 02-05-13
Completed: 19:48:06 02-05-13
Elapsed: 00 hrs 02 mins 48 secs

step 2. Correlate_Cluster_mutation_onlysig [id: 397797]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00503:3
cluster label file LUAD-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LUAD-TP/3145444/1.GDAC_mergedClustering.Finished/LUAD-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name LUAD-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:
 D4V3.png
 D5V3.pdf
 D5V3.png
 D5V8.pdf
 D4V3.pdf
 D5V8.png
 D5V7.pdf
 D4V7.pdf
 D5V7.png
 D4V7.png
 D6V7.pdf
 D6V8.png
 D6V7.png
 D6V8.pdf
 D10V8.pdf
 D10V8.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:45:18 02-05-13
Completed: 19:48:52 02-05-13
Elapsed: 00 hrs 03 mins 34 secs