MutSig_ClinicalAnalysis_nozzle Execution Log 8:31 PM Tue Jun 18, '13

Running as user: cgaadm_deadline

mutsig2cluster_new1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MergeMutSigRunResults/OV-TP/3584569/OV-TP.sample_sig_gene_table.txt
Correlate_Clinical_Clusters_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/OV-TP/3351705/OV-TP.clin.merged.picked.txt
Correlate_Clinical_Clusters_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Clusters_onlysig2 figure height 5
Correlate_Clinical_Clusters_onlysig2 figure width 9
Correlate_Clinical_Clusters_onlysig2 survival legend position OUT
Correlate_Clinical_Clusters_onlysig2 pvalue cutoff 1
Correlate_Clinical_Clusters_onlysig2 qvalue cutoff 0.25
Correlate_Clinical_Clusters_onlysig2 make figure ONLYSIG
Correlate_Clinical_Clusters_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 20:31:14 18-06-13
Completed:
Elapsed: 00 hrs 01 mins 22 secs

step 1. mutsig2cluster_new [id: 423595] 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/MergeMutSigRunResults/OV-TP/3584569/OV-TP.sample_sig_gene_table.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 OV-TP.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 20:31:18 18-06-13
Completed: 20:32:07 18-06-13
Elapsed: 00 hrs 00 mins 49 secs

step 2. Correlate_Clinical_Clusters_onlysig [id: 423596]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00335:81
cluster label file OV-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/OV-TP/3351705/OV-TP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name
figure height 5
figure width 9
survival legend position OUT
pvalue cutoff 1
qvalue cutoff 0.25
make figure ONLYSIG
nozzle ver Nozzle.R1
options MUTSIG
report title
job description
Output Files:
 table.1.txt
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 20:31:18 18-06-13
Completed: 20:32:36 18-06-13
Elapsed: 00 hrs 01 mins 17 secs