Mutsig_cluster_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_Cluster_mutation_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/THCA-TP/2909296/1.GDAC_mergedClustering.Finished/THCA-TP.transferedmergedcluster.txt
Correlate_Cluster_mutation_onlysig2 filter cluster smaller than 3
Correlate_Cluster_mutation_onlysig2 output name THCA-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: 10:54:13 09-04-13
Completed:
Elapsed: 01 hrs 33 mins 55 secs

step 1. mutsig2cluster_new [id: 376887] 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: 10:54:13 09-04-13
Completed: 12:26:13 09-04-13
Elapsed: 01 hrs 31 mins 59 secs

step 2. Correlate_Cluster_mutation_onlysig [id: 376888]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00503:3
cluster label file THCA-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/THCA-TP/2909296/1.GDAC_mergedClustering.Finished/THCA-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name THCA-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:
 D1V2.png
 D1V2.pdf
 D1V3.pdf
 D1V3.png
 D3V1.png
 D1V5.pdf
 D1V6.png
 D1V4.pdf
 D1V6.pdf
 D1V7.pdf
 D3V2.png
 D3V2.pdf
 D1V8.pdf
 D3V1.pdf
 D1V5.png
 D1V8.png
 D1V7.png
 D1V4.png
 D3V5.png
 D3V8.pdf
 D3V8.png
 D3V5.pdf
 D3V3.png
 D4V2.pdf
 D3V3.pdf
 D3V7.pdf
 D3V6.png
 D4V2.png
 D3V7.png
 D3V6.pdf
 D4V6.pdf
 D4V5.png
 D4V7.pdf
 D4V4.png
 D4V8.pdf
 D4V6.png
 D4V5.pdf
 D4V7.png
 D4V8.png
 D4V4.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:54:13 09-04-13
Completed: 12:28:07 09-04-13
Elapsed: 01 hrs 33 mins 54 secs