CNV_ClinicalAnalysis_nozzle Execution Log 6:52 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

cnv2cluster1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/HNSC-TP/2859794/all_lesions.conf_99.txt
Correlate_Clinical_Cnvs_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/HNSC-TP/2843134/1.GDAC_clinicalDataPicker.Finished/HNSC-TP.clin.merged.picked.txt
Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Cnvs_onlysig2 output name HNSC-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: 18:52:40 08-04-13
Completed:
Elapsed: 00 hrs 16 mins 29 secs

step 1. cnv2cluster [id: 373020] 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/HNSC-TP/2859794/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: 18:52:52 08-04-13
Completed: 18:54:26 08-04-13
Elapsed: 00 hrs 01 mins 34 secs

step 2. Correlate_Clinical_Cnvs_onlysig [id: 373021]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00495:48
cluster label file all_lesions.conf_99.cnv.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/HNSC-TP/2843134/1.GDAC_clinicalDataPicker.Finished/HNSC-TP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name HNSC-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:
 D23V3.pdf
 D23V3.png
 D32V1.pdf
 D32V1.png
 D33V10.pdf
 D33V10.png
 D34V10.png
 D34V10.pdf
 D35V9.pdf
 D35V9.png
 test_dim_tbl.txt
 table.1.txt
 nozzle.html
 nozzle.RData
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 18:52:52 08-04-13
Completed: 19:09:08 08-04-13
Elapsed: 00 hrs 16 mins 15 secs