MutSig_ClinicalAnalysis_nozzle Execution Log 10:52 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/COADREAD-TP/2862172/COADREAD-TP.sample_sig_gene_table.txt
Correlate_Clinical_Clusters_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/2843108/1.GDAC_clinicalDataPicker.Finished/COADREAD-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: 10:52:05 09-04-13
Completed:
Elapsed: 01 hrs 37 mins 51 secs

step 1. mutsig2cluster_new [id: 376810] 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/COADREAD-TP/2862172/COADREAD-TP.sample_sig_gene_table.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 COADREAD-TP.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:52:09 09-04-13
Completed: 12:26:46 09-04-13
Elapsed: 01 hrs 34 mins 37 secs

step 2. Correlate_Clinical_Clusters_onlysig [id: 376811]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00335:81
cluster label file COADREAD-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD-TP/2843108/1.GDAC_clinicalDataPicker.Finished/COADREAD-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:
 D3V11.pdf
 D3V11.png
 D5V5.pdf
 D5V5.png
 D14V11.pdf
 D14V11.png
 D22V11.png
 D22V11.pdf
 D32V11.pdf
 D32V11.png
 D35V11.png
 D36V11.pdf
 D35V11.pdf
 D36V11.png
 D39V11.png
 D39V11.pdf
 D48V11.pdf
 D48V11.png
 D70V11.pdf
 D70V11.png
 D71V11.pdf
 D71V11.png
 D88V11.png
 D88V11.pdf
 D91V11.png
 D91V11.pdf
 D94V11.png
 D94V11.pdf
 D99V11.pdf
 D99V11.png
 D118V11.png
 D118V11.pdf
 D120V1.png
 D120V1.pdf
 D126V11.png
 D126V11.pdf
 D129V11.pdf
 D129V11.png
 D134V11.png
 D134V11.pdf
 D143V11.pdf
 D143V11.png
 D151V11.png
 D151V11.pdf
 D163V11.pdf
 D163V11.png
 D170V11.png
 D170V11.pdf
 D180V11.pdf
 D180V11.png
 D185V11.pdf
 D185V11.png
 D190V11.png
 D190V11.pdf
 D202V11.pdf
 D202V11.png
 D205V11.png
 D205V11.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:52:09 09-04-13
Completed: 12:29:55 09-04-13
Elapsed: 01 hrs 37 mins 46 secs