MutSig_ClinicalAnalysis_nozzle Execution Log 10:51 AM Tue Apr 9, '13

Running as user: cgaadm_deadline

mutsig2cluster_new1 sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/COAD-TP/2862139/COAD-TP.sample_sig_gene_table.txt
Correlate_Clinical_Clusters_onlysig2 clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COAD-TP/2843117/1.GDAC_clinicalDataPicker.Finished/COAD-TP.clin.merged.picked.txt
Correlate_Clinical_Clusters_onlysig2 filter cluster smaller than 3
Correlate_Clinical_Clusters_onlysig2 figure height 5
Correlate_Clinical_Clusters_onlysig2 figure width 9
Correlate_Clinical_Clusters_onlysig2 survival legend position OUT
Correlate_Clinical_Clusters_onlysig2 pvalue cutoff 1
Correlate_Clinical_Clusters_onlysig2 qvalue cutoff 0.25
Correlate_Clinical_Clusters_onlysig2 make figure ONLYSIG
Correlate_Clinical_Clusters_onlysig2 nozzle ver Nozzle.R1
Execution Times:
Submitted: 10:51:50 09-04-13
Completed:
Elapsed: 01 hrs 36 mins 46 secs

step 1. mutsig2cluster_new [id: 376795] Convert mutsig results to cluster files

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00336:4
sample gene table file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/COAD-TP/2862139/COAD-TP.sample_sig_gene_table.txt
maf file
sig gene file
sig gene q cutoff 0.01
output name
Output Files:
 COAD-TP.mutsig.cluster.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:51:50 09-04-13
Completed: 12:25:38 09-04-13
Elapsed: 01 hrs 33 mins 47 secs

step 2. Correlate_Clinical_Clusters_onlysig [id: 376796]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00335:81
cluster label file COAD-TP.mutsig.cluster.txt
clinical info file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COAD-TP/2843117/1.GDAC_clinicalDataPicker.Finished/COAD-TP.clin.merged.picked.txt
features used ALL
filter cluster smaller than 3
output name
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:
 D2V4.png
 D2V4.pdf
 D19V10.png
 D19V10.pdf
 D32V10.png
 D32V10.pdf
 D35V10.pdf
 D35V10.png
 D44V10.png
 D44V10.pdf
 D47V10.png
 D47V10.pdf
 D52V2.png
 D52V2.pdf
 D61V10.pdf
 D61V10.png
 D66V10.pdf
 D66V10.png
 D68V10.png
 D68V10.pdf
 D76V10.pdf
 D76V10.png
 D84V1.png
 D84V1.pdf
 D87V10.png
 D87V10.pdf
 D94V10.pdf
 D95V10.pdf
 D94V10.png
 D95V10.png
 D96V10.png
 D96V10.pdf
 D97V10.pdf
 D97V10.png
 D100V10.png
 D100V10.pdf
 D102V10.png
 D102V10.pdf
 D105V2.pdf
 D105V2.png
 D111V10.png
 D111V10.pdf
 D115V10.png
 D115V10.pdf
 D118V10.pdf
 D118V10.png
 table.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 10:51:50 09-04-13
Completed: 12:28:35 09-04-13
Elapsed: 01 hrs 36 mins 44 secs