MutSig_ClinicalAnalysis_nozzle Execution Log 9:34 PM Thu Jan 10, '13

Running as user: cgaadm_deadline

mutsig2cluster_new1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/COAD-TP/2283923/0.MutSigRun.Finished/COAD-TP.sample_sig_gene_table.txt
Correlate_Clinical_Clusters_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COAD-TP/2172429/1.GDAC_clinicalDataPicker.Finished/COAD-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: 21:34:58 10-01-13
Completed:
Elapsed: 00 hrs 02 mins 53 secs

step 1. mutsig2cluster_new [id: 286912] 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/COAD-TP/2283923/0.MutSigRun.Finished/COAD-TP.sample_sig_gene_table.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 COAD-TP.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 21:34:59 10-01-13
Completed: 21:35:30 10-01-13
Elapsed: 00 hrs 00 mins 31 secs

step 2. Correlate_Clinical_Clusters_onlysig [id: 286913]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00335:36
cluster label file COAD-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COAD-TP/2172429/1.GDAC_clinicalDataPicker.Finished/COAD-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:
 D10V4.png
 D10V4.pdf
 D39V2.png
 D39V2.pdf
 D56V1.png
 D56V1.pdf
 D102V2.png
 D102V2.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 21:34:59 10-01-13
Completed: 21:37:51 10-01-13
Elapsed: 00 hrs 02 mins 52 secs