CNV_cluster_nozzle Execution Log 8:52 AM Wed Jun 12, '13

Running as user: cgaadm

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KIRC-TP/3471884/all_lesions.conf_99.txt
Correlate_Cluster_cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/KIRC-TP/3536964/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: 08:52:53 12-06-13
Completed:
Elapsed: 00 hrs 02 mins 08 secs

step 1. cnv2cluster [id: 421249] 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/3471884/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: 08:52:53 12-06-13
Completed: 08:53:25 12-06-13
Elapsed: 00 hrs 00 mins 31 secs

step 2. Correlate_Cluster_cnvs_onlysig [id: 421250]

    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/KIRC-TP/3536964/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:
 D1V7.pdf
 D1V9.pdf
 D1V3.pdf
 D1V9.png
 D1V3.png
 D1V7.png
 D2V9.png
 D2V3.png
 D2V8.png
 D2V7.png
 D2V9.pdf
 D2V8.pdf
 D2V7.pdf
 D2V3.pdf
 D3V8.pdf
 D3V4.pdf
 D3V8.png
 D3V3.png
 D3V3.pdf
 D3V7.pdf
 D3V6.png
 D3V7.png
 D3V4.png
 D3V6.pdf
 D3V10.pdf
 D3V9.pdf
 D3V10.png
 D3V9.png
 D5V8.pdf
 D5V8.png
 D6V5.png
 D5V10.pdf
 D5V10.png
 D6V3.png
 D6V3.pdf
 D6V5.pdf
 D6V7.pdf
 D7V3.png
 D7V3.pdf
 D7V5.pdf
 D6V7.png
 D7V4.png
 D7V4.pdf
 D7V5.png
 D7V10.pdf
 D7V7.pdf
 D7V9.png
 D7V8.png
 D7V11.png
 D7V11.pdf
 D7V12.pdf
 D7V8.pdf
 D7V10.png
 D7V12.png
 D7V9.pdf
 D7V7.png
 D14V1.png
 D14V2.png
 D14V2.pdf
 D14V1.pdf
 D14V3.pdf
 D14V3.png
 D14V5.png
 D14V8.pdf
 D14V6.pdf
 D14V10.pdf
 D14V9.pdf
 D14V7.pdf
 D14V9.png
 D14V10.png
 D14V7.png
 D14V8.png
 D14V6.png
 D14V5.pdf
 D15V3.png
 D15V3.pdf
 D15V2.png
 D15V2.pdf
 D14V12.png
 D14V12.pdf
 D15V5.pdf
 D15V10.pdf
 D15V10.png
 D15V5.png
 D15V9.pdf
 D15V9.png
 D16V3.png
 D16V10.pdf
 D16V3.pdf
 D16V10.png
 D18V3.png
 D17V10.pdf
 D17V8.pdf
 D17V7.pdf
 D17V8.png
 D17V7.png
 D18V1.png
 D18V2.pdf
 D18V1.pdf
 D18V2.png
 D17V10.png
 D18V4.png
 D18V5.png
 D18V8.pdf
 D18V3.pdf
 D18V5.pdf
 D18V4.pdf
 D18V8.png
 D18V9.png
 D18V9.pdf
 D18V7.pdf
 D18V7.png
 D19V3.pdf
 D19V2.png
 D19V5.pdf
 D19V2.pdf
 D18V10.png
 D18V12.png
 D18V10.pdf
 D19V3.png
 D19V1.pdf
 D19V4.pdf
 D18V12.pdf
 D19V4.png
 D19V1.png
 D19V5.png
 D19V8.png
 D19V12.pdf
 D19V9.pdf
 D19V7.png
 D19V7.pdf
 D19V8.pdf
 D19V10.png
 D19V12.png
 D19V9.png
 D19V10.pdf
 D20V3.png
 D20V3.pdf
 D20V7.pdf
 D20V7.png
 D20V8.pdf
 D20V10.png
 D20V10.pdf
 D20V8.png
 D21V3.pdf
 D21V3.png
 D22V3.png
 D21V8.pdf
 D21V8.png
 D22V3.pdf
 D23V3.pdf
 D23V3.png
 D24V3.png
 D24V4.png
 D24V8.pdf
 D24V7.png
 D24V3.pdf
 D24V4.pdf
 D24V8.png
 D24V7.pdf
 D25V5.png
 D25V7.png
 D25V3.pdf
 D25V3.png
 D25V9.pdf
 D25V7.pdf
 D25V5.pdf
 D25V9.png
 D25V12.pdf
 D25V11.pdf
 D25V11.png
 D25V12.png
 D26V3.png
 D26V3.pdf
 D26V5.png
 D26V11.pdf
 D26V11.png
 D26V5.pdf
 D26V12.png
 D26V9.png
 D26V12.pdf
 D26V7.pdf
 D26V7.png
 D26V9.pdf
 D27V3.pdf
 D27V3.png
 D28V2.png
 D28V5.png
 D28V2.pdf
 D28V3.pdf
 D28V7.pdf
 D28V3.png
 D28V4.png
 D28V5.pdf
 D28V4.pdf
 D28V7.png
 D28V11.pdf
 D28V11.png
 D28V10.pdf
 D28V8.png
 D28V9.png
 D28V8.pdf
 D28V12.pdf
 D28V10.png
 D28V12.png
 D28V9.pdf
 D29V4.png
 D29V3.png
 D29V2.png
 D29V2.pdf
 D29V3.pdf
 D29V6.png
 D29V5.png
 D29V6.pdf
 D29V5.pdf
 D29V4.pdf
 D29V8.pdf
 D29V11.pdf
 D29V7.pdf
 D29V7.png
 D29V8.png
 D29V12.pdf
 D29V9.pdf
 D29V9.png
 D29V12.png
 D29V10.png
 D29V10.pdf
 D29V11.png
 D30V3.png
 D30V3.pdf
 D31V7.png
 D31V8.png
 D31V5.png
 D31V9.png
 D31V3.pdf
 D31V8.pdf
 D31V3.png
 D31V5.pdf
 D31V7.pdf
 D31V4.png
 D31V4.pdf
 D31V10.png
 D32V1.pdf
 D32V2.pdf
 D32V2.png
 D32V3.png
 D31V10.pdf
 D32V1.png
 D32V3.pdf
 D31V12.png
 D31V9.pdf
 D31V12.pdf
 D32V4.png
 D32V6.png
 D32V7.png
 D32V7.pdf
 D32V5.pdf
 D32V6.pdf
 D32V5.png
 D32V4.pdf
 D32V11.pdf
 D32V8.png
 D32V8.pdf
 D32V9.png
 D32V11.png
 D32V9.pdf
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 08:52:53 12-06-13
Completed: 08:55:00 12-06-13
Elapsed: 00 hrs 02 mins 07 secs