MutSig_ClinicalAnalysis_nozzle Execution Log 3:23 PM Fri Jan 11, '13

Running as user: cgaadm_deadline

mutsig2cluster_new1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2288089/0.MutSigRun.Finished/SKCM-TM.sample_sig_gene_table.txt
Correlate_Clinical_Clusters_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM/2173730/1.GDAC_clinicalDataPicker.Finished/SKCM.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: 15:23:03 11-01-13
Completed:
Elapsed: 00 hrs 01 mins 47 secs

step 1. mutsig2cluster_new [id: 287508] 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/SKCM-TM/2288089/0.MutSigRun.Finished/SKCM-TM.sample_sig_gene_table.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 SKCM-TM.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:23:03 11-01-13
Completed: 15:24:18 11-01-13
Elapsed: 00 hrs 01 mins 14 secs

step 2. Correlate_Clinical_Clusters_onlysig [id: 287509]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00335:36
cluster label file SKCM-TM.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM/2173730/1.GDAC_clinicalDataPicker.Finished/SKCM.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:
 D60V1.pdf
 D60V1.png
 D82V1.pdf
 D82V1.png
 table.1.txt
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:23:03 11-01-13
Completed: 15:24:49 11-01-13
Elapsed: 00 hrs 01 mins 45 secs