CNV_cluster_nozzle Execution Log 9:53 AM Wed Jun 12, '13

Running as user: cgaadm

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BLCA-TP/3471805/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/BLCA-TP/3537480/BLCA-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name BLCA-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: 09:53:10 12-06-13
Completed:
Elapsed: 00 hrs 01 mins 59 secs

step 1. cnv2cluster [id: 421317] 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/BLCA-TP/3471805/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: 09:53:10 12-06-13
Completed: 09:53:37 12-06-13
Elapsed: 00 hrs 00 mins 26 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 421318]

    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_mergedClustering_new/BLCA-TP/3537480/BLCA-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name BLCA-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:
 D1V1.pdf
 D1V1.png
 D1V2.png
 D1V2.pdf
 D2V1.pdf
 D2V1.png
 D3V1.png
 D3V1.pdf
 D4V1.pdf
 D4V1.png
 D5V1.pdf
 D5V1.png
 D5V5.pdf
 D5V5.png
 D9V1.pdf
 D9V1.png
 D10V1.pdf
 D10V1.png
 D14V1.png
 D13V1.pdf
 D13V1.png
 D14V1.pdf
 D16V1.png
 D16V1.pdf
 D17V1.pdf
 D17V1.png
 D18V1.png
 D18V2.pdf
 D18V1.pdf
 D18V2.png
 D19V1.pdf
 D19V1.png
 D23V1.png
 D23V5.png
 D23V5.pdf
 D23V1.pdf
 D24V1.png
 D24V1.pdf
 D24V8.pdf
 D25V1.pdf
 D24V8.png
 D25V1.png
 D26V1.pdf
 D26V1.png
 D27V1.pdf
 D27V1.png
 D34V5.pdf
 D34V5.png
 D35V4.pdf
 D35V4.png
 D38V1.png
 D38V1.pdf
 D39V1.pdf
 D39V1.png
 D40V1.pdf
 D40V1.png
 D42V1.pdf
 D42V1.png
 D43V2.png
 D43V2.pdf
 D43V1.png
 D43V1.pdf
 D45V1.png
 D45V1.pdf
 D48V1.pdf
 D47V1.pdf
 D47V1.png
 D48V1.png
 D50V3.png
 D50V3.pdf
 D50V1.pdf
 D50V1.png
 D52V7.png
 D52V7.pdf
 D53V1.pdf
 D53V1.png
 D55V1.png
 D55V1.pdf
 D54V1.png
 D54V1.pdf
 D59V1.png
 D59V1.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 09:53:10 12-06-13
Completed: 09:55:08 12-06-13
Elapsed: 00 hrs 01 mins 57 secs