CNV_cluster_nozzle Execution Log 6:22 PM Mon Mar 4, '13

Running as user: cgaadm_deadline

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUSC-TP/2662124/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LUSC-TP/2666774/1.GDAC_mergedClustering.Finished/LUSC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name LUSC-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: 18:22:35 04-03-13
Completed:
Elapsed: 00 hrs 01 mins 42 secs

step 1. cnv2cluster [id: 335178] 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/LUSC-TP/2662124/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: 18:22:35 04-03-13
Completed: 18:22:59 04-03-13
Elapsed: 00 hrs 00 mins 24 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 335179]

    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/LUSC-TP/2666774/1.GDAC_mergedClustering.Finished/LUSC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name LUSC-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.pdf
 D1V3.png
 D2V3.png
 D2V3.pdf
 D3V1.png
 D3V4.pdf
 D3V3.png
 D3V3.pdf
 D3V7.pdf
 D3V1.pdf
 D3V7.png
 D3V4.png
 D4V3.pdf
 D4V4.png
 D4V4.pdf
 D4V3.png
 D6V10.png
 D6V7.pdf
 D6V2.pdf
 D6V8.png
 D6V4.pdf
 D6V7.png
 D6V8.pdf
 D6V2.png
 D6V4.png
 D6V3.png
 D6V3.pdf
 D9V3.png
 D8V3.pdf
 D6V10.pdf
 D9V3.pdf
 D8V3.png
 D12V4.png
 D12V3.png
 D12V3.pdf
 D12V4.pdf
 D18V3.png
 D18V3.pdf
 D22V3.png
 D22V4.png
 D22V4.pdf
 D22V3.pdf
 D22V10.pdf
 D23V3.pdf
 D23V3.png
 D23V4.png
 D23V4.pdf
 D22V10.png
 D25V3.pdf
 D25V3.png
 D24V3.pdf
 D24V3.png
 D26V3.png
 D26V3.pdf
 D28V3.pdf
 D28V3.png
 D32V1.pdf
 D32V4.png
 D32V2.pdf
 D32V2.png
 D32V3.png
 D32V1.png
 D32V3.pdf
 D32V4.pdf
 D32V8.png
 D33V1.pdf
 D33V3.pdf
 D33V4.pdf
 D33V4.png
 D32V8.pdf
 D33V3.png
 D32V7.png
 D32V7.pdf
 D33V1.png
 D33V8.png
 D33V7.pdf
 D33V7.png
 D33V8.pdf
 D36V2.pdf
 D36V2.png
 D35V3.pdf
 D36V1.png
 D36V1.pdf
 D35V3.png
 D36V3.png
 D36V4.pdf
 D36V7.pdf
 D36V7.png
 D36V4.png
 D36V3.pdf
 D36V8.pdf
 D36V8.png
 D39V3.pdf
 D39V4.pdf
 D39V4.png
 D39V3.png
 D38V3.pdf
 D38V3.png
 D40V3.pdf
 D40V3.png
 D42V3.pdf
 D42V3.png
 D44V4.pdf
 D44V3.png
 D44V10.png
 D43V3.pdf
 D44V3.pdf
 D44V4.png
 D44V10.pdf
 D43V3.png
 D45V3.png
 D45V4.pdf
 D45V4.png
 D45V3.pdf
 D51V3.png
 D51V3.pdf
 D53V2.pdf
 D52V3.pdf
 D53V3.png
 D53V1.pdf
 D52V3.png
 D53V2.png
 D53V1.png
 D53V10.png
 D53V8.pdf
 D53V4.png
 D53V7.pdf
 D53V10.pdf
 D53V4.pdf
 D53V7.png
 D53V8.png
 D53V3.pdf
 D55V3.pdf
 D55V4.png
 D55V7.pdf
 D55V4.pdf
 D55V8.png
 D55V7.png
 D55V8.pdf
 D55V3.png
 D56V3.pdf
 D56V3.png
 D56V6.png
 D56V6.pdf
 D67V1.png
 D67V2.png
 D67V7.png
 D67V1.pdf
 D67V8.pdf
 D67V2.pdf
 D67V7.pdf
 D67V3.pdf
 D67V3.png
 D67V8.png
 D70V3.pdf
 D70V3.png
 D71V3.png
 D71V4.png
 D72V3.png
 D72V3.pdf
 D71V3.pdf
 D71V4.pdf
 D74V3.pdf
 D74V3.png
 D76V3.png
 D76V3.pdf
 D77V3.png
 D77V3.pdf
 D78V3.png
 D78V3.pdf
 D78V4.pdf
 D78V4.png
 D79V3.png
 table.1.txt
 D79V3.pdf
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:22:35 04-03-13
Completed: 18:24:16 04-03-13
Elapsed: 00 hrs 01 mins 40 secs