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/LUSC-TP/2859876/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LUSC-TP/2909314/1.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: 10:05:42 09-04-13
Completed:
Elapsed: 00 hrs 03 mins 19 secs

step 1. cnv2cluster [id: 376247] 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/2859876/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: 10:05:55 09-04-13
Completed: 10:06:44 09-04-13
Elapsed: 00 hrs 00 mins 49 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 376248]

    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/2909314/1.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:
 D2V3.png
 D2V3.pdf
 D3V1.png
 D3V1.pdf
 D3V4.pdf
 D4V3.pdf
 D3V3.png
 D3V3.pdf
 D3V7.pdf
 D3V7.png
 D4V3.png
 D3V4.png
 D4V4.png
 D4V4.pdf
 D6V7.pdf
 D6V2.pdf
 D6V8.png
 D6V4.pdf
 D6V7.png
 D6V2.png
 D6V4.png
 D6V3.png
 D6V3.pdf
 D6V10.png
 D6V10.pdf
 D6V8.pdf
 D9V3.png
 D8V3.pdf
 D9V3.pdf
 D8V3.png
 D13V4.png
 D13V4.pdf
 D13V3.pdf
 D13V3.png
 D19V3.pdf
 D19V3.png
 D23V3.pdf
 D23V3.png
 D23V4.png
 D23V4.pdf
 D24V4.png
 D24V3.pdf
 D24V4.pdf
 D24V3.png
 D25V3.pdf
 D25V3.png
 D25V4.png
 D25V4.pdf
 D26V3.png
 D26V3.pdf
 D28V3.pdf
 D28V3.png
 D27V3.pdf
 D27V3.png
 D29V4.png
 D29V3.png
 D29V4.pdf
 D29V3.pdf
 D31V3.pdf
 D31V3.png
 D33V2.png
 D33V1.pdf
 D34V1.png
 D33V3.pdf
 D33V4.pdf
 D33V4.png
 D33V3.png
 D33V8.png
 D33V2.pdf
 D33V7.pdf
 D33V7.png
 D33V1.png
 D33V8.pdf
 D34V7.png
 D34V3.png
 D34V8.pdf
 D34V3.pdf
 D34V7.pdf
 D34V8.png
 D34V4.png
 D34V1.pdf
 D34V4.pdf
 D37V1.pdf
 D37V1.png
 D37V2.pdf
 D37V4.pdf
 D37V4.png
 D37V3.png
 D37V2.png
 D36V3.pdf
 D37V3.pdf
 D36V3.png
 D37V7.pdf
 D37V8.png
 D37V7.png
 D37V8.pdf
 D39V3.pdf
 D40V3.pdf
 D40V3.png
 D39V3.png
 D42V3.pdf
 D43V3.pdf
 D43V3.png
 D42V3.png
 D44V3.png
 D44V3.pdf
 D46V3.pdf
 D45V3.png
 D45V4.pdf
 D46V3.png
 D45V4.png
 D45V3.pdf
 D46V10.png
 D47V3.pdf
 D46V4.png
 D47V4.png
 D47V4.pdf
 D46V10.pdf
 D47V3.png
 D46V4.pdf
 D51V3.png
 D51V3.pdf
 D54V3.pdf
 D54V3.png
 D56V3.pdf
 D56V3.png
 D55V3.pdf
 D56V1.png
 D56V1.pdf
 D56V2.pdf
 D56V4.png
 D56V2.png
 D55V3.png
 D56V4.pdf
 D56V7.pdf
 D56V10.pdf
 D57V4.pdf
 D57V4.png
 D57V3.png
 D56V10.png
 D57V3.pdf
 D56V8.png
 D56V8.pdf
 D56V7.png
 D58V7.png
 D58V3.png
 D58V4.pdf
 D58V7.pdf
 D58V4.png
 D58V3.pdf
 D59V3.pdf
 D59V7.pdf
 D59V8.png
 D59V3.png
 D59V4.pdf
 D59V7.png
 D59V8.pdf
 D59V4.png
 D60V3.png
 D60V3.pdf
 D60V6.pdf
 D60V6.png
 D72V1.png
 D72V7.pdf
 D72V2.png
 D72V8.pdf
 D72V3.png
 D72V1.pdf
 D72V2.pdf
 D72V8.png
 D72V3.pdf
 D72V7.png
 D75V3.pdf
 D75V3.png
 D76V3.png
 D76V4.png
 D76V3.pdf
 D76V4.pdf
 D78V3.png
 D78V3.pdf
 D80V1.pdf
 D80V1.png
 D80V2.pdf
 D80V2.png
 D81V3.png
 D81V3.pdf
 D82V3.pdf
 D82V3.png
 D83V3.png
 D82V4.png
 D82V4.pdf
 D83V3.pdf
 D83V4.png
 D83V4.pdf
 D84V4.pdf
 D84V4.png
 D84V3.png
 D84V3.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:05:55 09-04-13
Completed: 10:09:00 09-04-13
Elapsed: 00 hrs 03 mins 05 secs