MutSig_ClinicalAnalysis_nozzle Execution Log 10:54 AM Tue Apr 9, '13

Running as user: cgaadm_deadline

mutsig2cluster_new1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/THCA-TP/2863008/THCA-TP.sample_sig_gene_table.txt
Correlate_Clinical_Clusters_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2844384/1.GDAC_clinicalDataPicker.Finished/THCA-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: 10:54:13 09-04-13
Completed:
Elapsed: 01 hrs 34 mins 20 secs

step 1. mutsig2cluster_new [id: 376897] 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/THCA-TP/2863008/THCA-TP.sample_sig_gene_table.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 THCA-TP.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:54:16 09-04-13
Completed: 12:26:10 09-04-13
Elapsed: 01 hrs 31 mins 53 secs

step 2. Correlate_Clinical_Clusters_onlysig [id: 376898]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00335:81
cluster label file THCA-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2844384/1.GDAC_clinicalDataPicker.Finished/THCA-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:
 D1V3.pdf
 D1V3.png
 D1V7.pdf
 D1V8.pdf
 D1V8.png
 D1V7.png
 D3V3.png
 D3V3.pdf
 D4V3.pdf
 D4V3.png
 D7V8.png
 D7V8.pdf
 D17V10.pdf
 D17V14.pdf
 D17V14.png
 D17V10.png
 table.1.txt
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:54:16 09-04-13
Completed: 12:28:32 09-04-13
Elapsed: 01 hrs 34 mins 15 secs