CNV_cluster_nozzle Execution Log 9:50 AM Tue Apr 9, '13

Running as user: cgaadm_deadline

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/CESC-TP/2859755/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/CESC-TP/2907374/1.GDAC_mergedClustering.Finished/CESC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name CESC-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: 09:50:35 09-04-13
Completed:
Elapsed: 00 hrs 02 mins 39 secs

step 1. cnv2cluster [id: 375834] 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/CESC-TP/2859755/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: 09:50:40 09-04-13
Completed: 09:52:12 09-04-13
Elapsed: 00 hrs 01 mins 32 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 375835]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00507:2
cluster label file all_lesions.conf_99.cnv.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/CESC-TP/2907374/1.GDAC_mergedClustering.Finished/CESC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name CESC-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:
 D4V1.pdf
 D4V1.png
 D4V3.pdf
 D5V1.pdf
 D5V1.png
 D6V1.pdf
 D6V1.png
 D4V3.png
 D14V1.png
 D14V1.pdf
 D25V6.pdf
 D25V6.png
 D29V1.png
 D29V1.pdf
 D30V1.png
 D30V1.pdf
 D31V1.png
 D31V1.pdf
 D38V1.png
 D38V1.pdf
 D43V1.png
 D43V1.pdf
 D45V3.png
 D45V4.pdf
 D45V4.png
 D45V3.pdf
 D45V6.png
 D45V6.pdf
 D48V6.pdf
 D48V6.png
 table.1.txt
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 09:50:40 09-04-13
Completed: 09:53:14 09-04-13
Elapsed: 00 hrs 02 mins 34 secs