CNV_ClinicalAnalysis_nozzle Execution Log 4:32 PM Thu May 23, '13

Running as user: cgaadm

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/COAD-TP/3140322/all_lesions.conf_99.txt
Correlate_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COAD-TP/3132635/1.GDAC_clinicalDataPicker.Finished/COAD-TP.clin.merged.picked.txt
Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvs_onlysig2 output name COAD-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: 16:32:35 23-05-13
Completed:
Elapsed: 00 hrs 10 mins 00 secs

step 1. cnv2cluster [id: 410795] 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/COAD-TP/3140322/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: 16:32:36 23-05-13
Completed: 16:33:03 23-05-13
Elapsed: 00 hrs 00 mins 27 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 410796]

    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/COAD-TP/3132635/1.GDAC_clinicalDataPicker.Finished/COAD-TP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name COAD-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:
 D11V4.png
 D11V4.pdf
 D12V4.png
 D12V4.pdf
 D12V8.pdf
 D12V8.png
 D13V6.pdf
 D13V6.png
 D13V8.png
 D13V8.pdf
 D14V6.png
 D14V6.pdf
 D14V8.png
 D14V8.pdf
 D22V4.png
 D22V4.pdf
 D23V4.png
 D23V4.pdf
 D24V4.png
 D24V4.pdf
 D25V7.png
 D25V7.pdf
 D33V1.pdf
 D33V1.png
 D33V6.pdf
 D33V6.png
 D33V7.pdf
 D33V7.png
 D37V6.png
 D37V6.pdf
 D42V6.png
 D42V6.pdf
 D42V8.png
 D42V8.pdf
 D43V6.png
 D43V6.pdf
 D43V8.png
 D43V8.pdf
 D45V6.png
 D45V6.pdf
 D52V7.png
 D52V7.pdf
 D59V4.png
 D59V4.pdf
 D59V6.png
 D59V8.png
 D59V6.pdf
 D59V11.png
 D59V8.pdf
 D59V11.pdf
 D61V4.png
 D61V4.pdf
 D62V4.pdf
 D62V4.png
 D63V4.png
 D63V6.pdf
 D63V4.pdf
 D63V6.png
 D63V8.png
 D63V8.pdf
 D64V4.pdf
 D64V4.png
 D64V6.png
 D64V6.pdf
 D64V8.png
 D64V8.pdf
 D65V6.png
 D65V6.pdf
 test_dim_tbl.txt
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 16:32:36 23-05-13
Completed: 16:42:34 23-05-13
Elapsed: 00 hrs 09 mins 58 secs