CNV_ClinicalAnalysis_nozzle Execution Log 1:26 AM Fri Mar 29, '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_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRC-TP/2587686/1.GDAC_clinicalDataPicker.Finished/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: 01:26:50 29-03-13
Completed:
Elapsed: 00 hrs 02 mins 49 secs

step 1. cnv2cluster [id: 351828] 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: 01:26:50 29-03-13
Completed: 01:27:22 29-03-13
Elapsed: 00 hrs 00 mins 31 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 351829]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00495:47
cluster label file all_lesions.conf_99.cnv.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRC-TP/2587686/1.GDAC_clinicalDataPicker.Finished/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
 D3V5.pdf
 D3V7.pdf
 D3V7.png
 D3V8.png
 D3V8.pdf
 D7V5.png
 D7V5.pdf
 D18V5.png
 D18V8.pdf
 D18V5.pdf
 D18V8.png
 D20V3.png
 D20V3.pdf
 D21V1.png
 D21V5.png
 D21V5.pdf
 D21V1.pdf
 D21V8.pdf
 D21V8.png
 D25V1.pdf
 D25V1.png
 D25V5.png
 D25V7.png
 D25V7.pdf
 D25V8.png
 D25V5.pdf
 D25V8.pdf
 D26V1.pdf
 D26V1.png
 D26V8.pdf
 D26V5.pdf
 D26V8.png
 D26V7.pdf
 D26V7.png
 D26V5.png
 D27V5.png
 D27V5.pdf
 D28V5.png
 D28V1.pdf
 D28V5.pdf
 D28V1.png
 D28V8.png
 D28V8.pdf
 D29V6.png
 D29V5.png
 D29V6.pdf
 D29V5.pdf
 D29V8.pdf
 D29V7.pdf
 D29V7.png
 D29V8.png
 test_dim_tbl.txt
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 01:26:50 29-03-13
Completed: 01:29:38 29-03-13
Elapsed: 00 hrs 02 mins 47 secs