CNV_ClinicalAnalysis_nozzle Execution Log 4:33 PM Thu May 23, '13

Running as user: cgaadm

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUAD-TP/3140812/all_lesions.conf_99.txt
Correlate_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUAD-TP/3132696/1.GDAC_clinicalDataPicker.Finished/LUAD-TP.clin.merged.picked.txt
Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvs_onlysig2 output name LUAD-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: 16:33:06 23-05-13
Completed:
Elapsed: 00 hrs 02 mins 25 secs

step 1. cnv2cluster [id: 410831] 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/LUAD-TP/3140812/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: 16:33:06 23-05-13
Completed: 16:33:38 23-05-13
Elapsed: 00 hrs 00 mins 31 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 410832]

    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_clinicalDataPickerPipeline/LUAD-TP/3132696/1.GDAC_clinicalDataPicker.Finished/LUAD-TP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name LUAD-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:
 D17V12.pdf
 D17V12.png
 D18V2.pdf
 D18V2.png
 D37V13.png
 D37V13.pdf
 D44V12.png
 D44V12.pdf
 D55V3.pdf
 D55V3.png
 D75V3.pdf
 D75V3.png
 D76V9.pdf
 D76V9.png
 test_dim_tbl.txt
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 16:33:06 23-05-13
Completed: 16:35:30 23-05-13
Elapsed: 00 hrs 02 mins 23 secs