Mutsig_cluster_nozzle Execution Log 8:20 PM Thu May 2, '13

Running as user: cgaadm_deadline

mutsig2cluster_new1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-TM/2862710/SKCM-TM.sample_sig_gene_table.txt
Correlate_Cluster_mutation_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-TM/3147601/1.GDAC_mergedClustering.Finished/SKCM-TM.transferedmergedcluster.txt
Correlate_Cluster_mutation_onlysig2 filter cluster smaller than 3
Correlate_Cluster_mutation_onlysig2 output name SKCM-TM
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: 20:20:55 02-05-13
Completed:
Elapsed: 00 hrs 02 mins 06 secs

step 1. mutsig2cluster_new [id: 397888] 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/SKCM-TM/2862710/SKCM-TM.sample_sig_gene_table.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 SKCM-TM.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 20:20:55 02-05-13
Completed: 20:22:17 02-05-13
Elapsed: 00 hrs 01 mins 21 secs

step 2. Correlate_Cluster_mutation_onlysig [id: 397889]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00503:3
cluster label file SKCM-TM.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-TM/3147601/1.GDAC_mergedClustering.Finished/SKCM-TM.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name SKCM-TM
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:
 D2V1.pdf
 D2V1.png
 D2V6.pdf
 D2V6.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 20:20:55 02-05-13
Completed: 20:23:01 02-05-13
Elapsed: 00 hrs 02 mins 05 secs