CNV_cluster_nozzle Execution Log 10:05 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/KIRP-TP/2859841/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRP-TP/2909316/1.GDAC_mergedClustering.Finished/KIRP-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name KIRP-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: 10:05:37 09-04-13
Completed:
Elapsed: 00 hrs 03 mins 30 secs

step 1. cnv2cluster [id: 376223] 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/KIRP-TP/2859841/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: 10:05:40 09-04-13
Completed: 10:07:04 09-04-13
Elapsed: 00 hrs 01 mins 23 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 376224]

    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/KIRP-TP/2909316/1.GDAC_mergedClustering.Finished/KIRP-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name KIRP-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:
 D1V3.png
 D2V3.png
 D1V3.pdf
 D2V3.pdf
 D3V3.png
 D2V8.png
 D2V6.pdf
 D2V8.pdf
 D2V6.png
 D3V3.pdf
 D3V6.png
 D3V6.pdf
 D4V3.png
 D4V3.pdf
 D6V3.png
 D6V3.pdf
 D6V6.pdf
 D6V6.png
 D6V4.pdf
 D6V4.png
 D7V3.png
 D7V3.pdf
 D8V3.pdf
 D8V3.png
 D10V3.png
 D10V3.pdf
 D13V4.png
 D13V4.pdf
 D13V3.pdf
 D13V3.png
 D14V3.pdf
 D14V3.png
 D14V4.pdf
 D14V4.png
 D16V3.pdf
 D16V3.png
 D17V3.pdf
 D17V3.png
 D17V5.pdf
 D17V5.png
 D17V6.png
 D17V6.pdf
 D18V3.png
 D18V3.pdf
 D20V3.png
 D20V3.pdf
 D21V3.pdf
 D21V3.png
 D21V4.png
 D21V4.pdf
 D21V5.png
 D21V5.pdf
 D24V3.png
 D25V3.png
 D24V3.pdf
 D25V3.pdf
 D26V3.png
 D26V3.pdf
 D31V3.pdf
 D31V3.png
 D31V4.png
 D31V4.pdf
 D32V3.png
 D32V3.pdf
 D33V3.pdf
 D33V3.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:05:40 09-04-13
Completed: 10:09:07 09-04-13
Elapsed: 00 hrs 03 mins 26 secs