CNV_cluster_nozzle Execution Log 1:53 PM Fri May 24, '13

Running as user: cgaadm

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LIHC-TP/3140751/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LIHC-TP/3144268/1.GDAC_mergedClustering.Finished/LIHC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name LIHC-TP
Correlate_Cluster_cnvs_onlysig2 figure height 5
Correlate_Cluster_cnvs_onlysig2 figure width 9
Correlate_Cluster_cnvs_onlysig2 survival legend position OUT
Correlate_Cluster_cnvs_onlysig2 pvalue cutoff 1
Correlate_Cluster_cnvs_onlysig2 qvalue cutoff 0.25
Correlate_Cluster_cnvs_onlysig2 make figure ONLYSIG
Correlate_Cluster_cnvs_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 13:53:01 24-05-13
Completed:
Elapsed: 00 hrs 01 mins 11 secs

step 1. cnv2cluster [id: 411564] Convert mutsig results to cluster files

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00494:12
sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LIHC-TP/3140751/all_lesions.conf_99.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 all_lesions.conf_99.cnv.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:53:01 24-05-13
Completed: 13:53:14 24-05-13
Elapsed: 00 hrs 00 mins 13 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 411565]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00507:4
cluster label file all_lesions.conf_99.cnv.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LIHC-TP/3144268/1.GDAC_mergedClustering.Finished/LIHC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name LIHC-TP
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:
 D2V2.pdf
 D2V2.png
 D11V2.png
 D11V2.pdf
 D14V1.png
 D15V1.pdf
 D15V1.png
 D14V1.pdf
 D18V1.png
 D18V1.pdf
 D24V1.png
 D24V1.pdf
 D30V4.png
 D31V1.png
 D30V4.pdf
 D31V1.pdf
 D36V1.png
 D36V1.pdf
 D47V1.pdf
 D47V1.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 13:53:01 24-05-13
Completed: 13:54:11 24-05-13
Elapsed: 00 hrs 01 mins 10 secs