Mutsig_cluster_nozzle Execution Log 10:51 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/COAD-TP/2862139/COAD-TP.sample_sig_gene_table.txt
Correlate_Cluster_mutation_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/COAD-TP/2909319/1.GDAC_mergedClustering.Finished/COAD-TP.transferedmergedcluster.txt
Correlate_Cluster_mutation_onlysig2 filter cluster smaller than 3
Correlate_Cluster_mutation_onlysig2 output name COAD-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: 10:51:49 09-04-13
Completed:
Elapsed: 01 hrs 36 mins 22 secs

step 1. mutsig2cluster_new [id: 376789] 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/2862139/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: 10:51:49 09-04-13
Completed: 12:25:36 09-04-13
Elapsed: 01 hrs 33 mins 46 secs

step 2. Correlate_Cluster_mutation_onlysig [id: 376790]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00503:3
cluster label file COAD-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/COAD-TP/2909319/1.GDAC_mergedClustering.Finished/COAD-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name COAD-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:
 D2V2.pdf
 D2V3.png
 D2V2.png
 D2V1.pdf
 D2V1.png
 D2V3.pdf
 D7V3.png
 D7V3.pdf
 D17V3.pdf
 D17V3.png
 D48V1.pdf
 D48V1.png
 D48V3.pdf
 D48V3.png
 D60V1.png
 D61V2.pdf
 D60V1.pdf
 D61V2.png
 D82V2.png
 D82V2.pdf
 D110V3.pdf
 D110V3.png
 D110V1.png
 D110V1.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:51:50 09-04-13
Completed: 12:28:10 09-04-13
Elapsed: 01 hrs 36 mins 20 secs