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/PRAD-TP/2859911/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/PRAD-TP/2907382/1.GDAC_mergedClustering.Finished/PRAD-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name PRAD-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: 09:50:37 09-04-13
Completed:
Elapsed: 00 hrs 02 mins 35 secs

step 1. cnv2cluster [id: 375849] 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/PRAD-TP/2859911/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: 09:52:11 09-04-13
Elapsed: 00 hrs 01 mins 30 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 375850]

    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/PRAD-TP/2907382/1.GDAC_mergedClustering.Finished/PRAD-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name PRAD-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:
 D2V1.pdf
 D2V1.png
 D3V1.png
 D4V1.pdf
 D4V4.png
 D3V1.pdf
 D4V1.png
 D4V4.pdf
 D7V1.pdf
 D7V1.png
 D5V1.pdf
 D5V1.png
 D6V1.pdf
 D6V1.png
 D22V2.pdf
 D22V2.png
 D26V1.png
 D26V1.pdf
 D30V1.png
 D30V1.pdf
 D29V2.png
 D29V1.png
 D30V2.png
 D29V2.pdf
 D29V1.pdf
 D31V2.pdf
 D31V1.png
 D31V2.png
 D31V1.pdf
 D30V2.pdf
 D32V1.pdf
 D32V4.png
 D34V1.png
 D34V2.png
 D32V2.pdf
 D32V2.png
 D32V3.png
 D34V1.pdf
 D32V1.png
 D32V3.pdf
 D32V5.pdf
 D32V5.png
 D32V4.pdf
 D34V3.png
 D34V3.pdf
 D35V2.pdf
 D35V3.pdf
 D34V2.pdf
 D34V4.png
 D34V4.pdf
 D35V2.png
 D35V3.png
 D37V1.pdf
 D37V1.png
 D37V2.pdf
 D37V4.pdf
 D37V4.png
 D37V3.png
 D37V2.png
 D36V1.png
 D37V3.pdf
 D36V1.pdf
 D39V1.pdf
 D39V1.png
 D40V1.pdf
 D40V1.png
 D41V1.pdf
 D42V1.pdf
 D41V1.png
 D42V1.png
 D43V2.png
 D43V2.pdf
 D44V1.pdf
 D43V3.pdf
 D43V4.pdf
 D43V4.png
 D43V3.png
 D44V1.png
 D46V2.pdf
 D46V2.png
 D46V3.pdf
 D46V1.png
 D46V1.pdf
 D45V1.png
 D46V4.png
 D46V3.png
 D45V1.pdf
 D46V4.pdf
 D47V1.pdf
 D47V2.png
 D47V1.png
 D47V6.png
 D47V2.pdf
 D47V3.pdf
 D47V4.png
 D47V4.pdf
 table.1.txt
 D47V6.pdf
 D47V3.png
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 09:50:40 09-04-13
Completed: 09:53:11 09-04-13
Elapsed: 00 hrs 02 mins 30 secs