Mutsig_cluster_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_Cluster_mutation_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/COADREAD-TP/2909317/1.GDAC_mergedClustering.Finished/COADREAD-TP.transferedmergedcluster.txt
Correlate_Cluster_mutation_onlysig2 filter cluster smaller than 3
Correlate_Cluster_mutation_onlysig2 output name COADREAD-TP
Correlate_Cluster_mutation_onlysig2 figure height 5
Correlate_Cluster_mutation_onlysig2 figure width 9
Correlate_Cluster_mutation_onlysig2 survival legend position OUT
Correlate_Cluster_mutation_onlysig2 pvalue cutoff 0.05
Correlate_Cluster_mutation_onlysig2 qvalue cutoff 0.25
Correlate_Cluster_mutation_onlysig2 make figure ONLYSIG
Correlate_Cluster_mutation_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 10:52:05 09-04-13
Completed:
Elapsed: 01 hrs 37 mins 36 secs

step 1. mutsig2cluster_new [id: 376805] 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: 10:52:05 09-04-13
Completed: 12:25:42 09-04-13
Elapsed: 01 hrs 33 mins 36 secs

step 2. Correlate_Cluster_mutation_onlysig [id: 376806]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00503:3
cluster label file COADREAD-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/COADREAD-TP/2909317/1.GDAC_mergedClustering.Finished/COADREAD-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name COADREAD-TP
figure height 5
figure width 9
survival legend position OUT
pvalue cutoff 0.05
qvalue cutoff 0.25
make figure ONLYSIG
nozzle ver Nozzle.R1
options MUTSIG
report title
job description
Output Files:
 D1V3.pdf
 D1V3.png
 D5V3.pdf
 D5V3.png
 D5V2.pdf
 D5V1.pdf
 D5V1.png
 D5V2.png
 D8V3.pdf
 D8V3.png
 D13V3.pdf
 D13V3.png
 D35V1.png
 D35V1.pdf
 D40V1.pdf
 D40V1.png
 D51V3.png
 D51V3.pdf
 D58V1.pdf
 D58V1.png
 D89V6.pdf
 D89V6.png
 D100V2.png
 D100V2.pdf
 D109V2.pdf
 D109V3.png
 D109V2.png
 D109V3.pdf
 D119V1.png
 D119V1.pdf
 D119V3.pdf
 D119V3.png
 D138V1.pdf
 D138V1.png
 D142V1.png
 D142V2.pdf
 D142V2.png
 D142V1.pdf
 D138V3.png
 D142V3.png
 D138V3.pdf
 D142V3.pdf
 D184V6.png
 D184V6.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:52:05 09-04-13
Completed: 12:29:39 09-04-13
Elapsed: 01 hrs 37 mins 34 secs