CNV_cluster_nozzle Execution Log 8:04 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/KIRC-TP/2661799/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRC-TP/2666908/1.GDAC_mergedClustering.Finished/KIRC-TP.transferedmergedcluster.txt
Correlate_Cluster_cnvs_onlysig2 filter cluster smaller than 3
Correlate_Cluster_cnvs_onlysig2 output name KIRC-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: 20:04:20 04-03-13
Completed:
Elapsed: 00 hrs 01 mins 37 secs

step 1. cnv2cluster [id: 335358] 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/KIRC-TP/2661799/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: 20:04:20 04-03-13
Completed: 20:05:00 04-03-13
Elapsed: 00 hrs 00 mins 39 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 335359]

    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/KIRC-TP/2666908/1.GDAC_mergedClustering.Finished/KIRC-TP.transferedmergedcluster.txt
features used ALL
filter cluster smaller than 3
output name KIRC-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
 D2V7.png
 D1V7.pdf
 D1V9.pdf
 D1V8.pdf
 D1V9.png
 D2V5.pdf
 D1V8.png
 D2V5.png
 D2V7.pdf
 D1V7.png
 D2V3.pdf
 D3V5.png
 D3V8.pdf
 D3V4.pdf
 D3V8.png
 D3V5.pdf
 D2V9.png
 D3V3.png
 D2V8.png
 D3V3.pdf
 D2V9.pdf
 D3V7.pdf
 D2V8.pdf
 D3V6.png
 D3V7.png
 D3V4.png
 D3V6.pdf
 D5V3.pdf
 D5V3.png
 D3V9.pdf
 D3V9.png
 D5V8.pdf
 D6V7.pdf
 D6V5.png
 D5V8.png
 D6V7.png
 D6V3.png
 D6V3.pdf
 D6V5.pdf
 D7V7.pdf
 D7V9.png
 D7V8.png
 D7V6.png
 D7V3.png
 D7V3.pdf
 D7V5.pdf
 D7V4.png
 D7V4.pdf
 D7V5.png
 D7V6.pdf
 D7V8.pdf
 D7V7.png
 D7V10.pdf
 D7V10.png
 D7V9.pdf
 D13V1.pdf
 D13V9.pdf
 D13V2.png
 D13V5.png
 D13V9.png
 D13V1.png
 D13V6.pdf
 D13V8.png
 D13V3.pdf
 D13V2.pdf
 D13V7.png
 D13V7.pdf
 D13V5.pdf
 D13V8.pdf
 D13V6.png
 D13V3.png
 D14V9.pdf
 D14V9.png
 D13V10.pdf
 D14V2.png
 D14V2.pdf
 D14V10.png
 D14V3.pdf
 D13V10.png
 D14V3.png
 D14V10.pdf
 D15V10.pdf
 D15V10.png
 D16V10.pdf
 D17V4.png
 D17V7.pdf
 D17V3.pdf
 D17V1.pdf
 D17V2.png
 D17V4.pdf
 D17V7.png
 D17V1.png
 D16V8.pdf
 D16V7.pdf
 D16V7.png
 D16V8.png
 D17V2.pdf
 D16V10.png
 D17V3.png
 D18V6.png
 D18V3.png
 D17V10.pdf
 D17V8.pdf
 D17V9.pdf
 D17V8.png
 D18V3.pdf
 D17V9.png
 D18V6.pdf
 D18V1.png
 D18V8.png
 D18V2.pdf
 D18V1.pdf
 D18V2.png
 D17V10.png
 D18V7.pdf
 D18V7.png
 D19V3.pdf
 D19V8.png
 D18V10.png
 D18V8.pdf
 D19V8.pdf
 D18V10.pdf
 D19V3.png
 D18V9.png
 D18V9.pdf
 D20V3.png
 D20V3.pdf
 D21V3.pdf
 D21V3.png
 D21V4.png
 D21V7.png
 D22V5.pdf
 D22V3.png
 D21V7.pdf
 D21V8.pdf
 D21V8.png
 D22V3.pdf
 D22V5.png
 D21V4.pdf
 D23V3.pdf
 D23V3.png
 D22V6.png
 D22V9.png
 D22V7.png
 D23V5.png
 D22V7.pdf
 D23V5.pdf
 D22V9.pdf
 D22V6.pdf
 D23V6.pdf
 D23V9.png
 D23V7.pdf
 D23V9.pdf
 D24V3.pdf
 D24V3.png
 D23V6.png
 D23V7.png
 D25V5.png
 D25V7.png
 D25V3.pdf
 D25V3.png
 D25V4.png
 D25V4.pdf
 D25V7.pdf
 D24V9.png
 D24V9.pdf
 D25V8.png
 D25V5.pdf
 D25V8.pdf
 D26V1.pdf
 D26V4.pdf
 D26V1.png
 D25V10.pdf
 D26V4.png
 D26V2.png
 D26V2.pdf
 D26V8.pdf
 D25V9.pdf
 D26V5.pdf
 D26V8.png
 D26V7.pdf
 D26V7.png
 D26V3.png
 D25V10.png
 D26V3.pdf
 D25V9.png
 D26V5.png
 D26V10.png
 D27V3.pdf
 D26V9.png
 D27V3.png
 D26V10.pdf
 D26V9.pdf
 D28V5.png
 D28V3.pdf
 D28V7.pdf
 D28V10.pdf
 D28V3.png
 D28V8.png
 D28V4.png
 D28V9.png
 D28V5.pdf
 D28V8.pdf
 D28V4.pdf
 D28V10.png
 D29V1.png
 D28V7.png
 D28V9.pdf
 D29V1.pdf
 D29V8.pdf
 D29V6.png
 D29V7.pdf
 D29V7.png
 D29V8.png
 D29V5.png
 D29V9.pdf
 D29V9.png
 D29V6.pdf
 D29V4.png
 D29V3.png
 D29V2.png
 D29V5.pdf
 D29V2.pdf
 D29V4.pdf
 D29V3.pdf
 D30V4.png
 D30V6.png
 D30V6.pdf
 D30V4.pdf
 D30V10.png
 table.1.txt
 D30V3.png
 D30V3.pdf
 D30V10.pdf
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 20:04:20 04-03-13
Completed: 20:05:57 04-03-13
Elapsed: 00 hrs 01 mins 36 secs