CNV_ClinicalAnalysis_nozzle Execution Log 11:50 AM Thu Jun 6, '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_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRC-TP/3351227/KIRC-TP.clin.merged.picked.txt
Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvs_onlysig2 output name KIRC-TP
Correlate_Clinical_Cnvs_onlysig2 figure height 5
Correlate_Clinical_Cnvs_onlysig2 figure width 9
Correlate_Clinical_Cnvs_onlysig2 survival legend position OUT
Correlate_Clinical_Cnvs_onlysig2 pvalue cutoff 1
Correlate_Clinical_Cnvs_onlysig2 qvalue cutoff 0.25
Correlate_Clinical_Cnvs_onlysig2 make figure ONLYSIG
Correlate_Clinical_Cnvs_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 11:50:24 06-06-13
Completed:
Elapsed: 00 hrs 02 mins 39 secs

step 1. cnv2cluster [id: 417159] 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: 11:50:24 06-06-13
Completed: 11:51:34 06-06-13
Elapsed: 00 hrs 01 mins 09 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 417160]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00495:49
cluster label file all_lesions.conf_99.cnv.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRC-TP/3351227/KIRC-TP.clin.merged.picked.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:
 D3V5.png
 D3V8.pdf
 D3V8.png
 D3V5.pdf
 D7V8.png
 D7V8.pdf
 D22V3.png
 D22V3.pdf
 D23V3.pdf
 D23V3.png
 D24V1.png
 D24V8.pdf
 D24V8.png
 D24V1.pdf
 D28V1.pdf
 D28V1.png
 D28V5.png
 D28V8.png
 D28V5.pdf
 D28V8.pdf
 D29V5.png
 D29V3.png
 D29V1.png
 D29V5.pdf
 D29V1.pdf
 D29V3.pdf
 D29V8.pdf
 D29V8.png
 D31V1.png
 D31V1.pdf
 D31V8.png
 D31V8.pdf
 test_dim_tbl.txt
 D32V8.png
 D32V6.png
 D32V8.pdf
 D32V5.pdf
 D32V6.pdf
 D32V5.png
 table.1.txt
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 11:50:24 06-06-13
Completed: 11:53:02 06-06-13
Elapsed: 00 hrs 02 mins 38 secs