zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R

This commit is contained in:
Mark DePristo 2011-12-19 10:08:38 -05:00
parent 5b678e3b94
commit 5383c50654
1 changed files with 7 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R
View File

@ -12,7 +12,7 @@ if ( onCMDLine ) {
inputFileName = args[1] inputFileName = args[1]
outputPDF = args[2] outputPDF = args[2]
} else { } else {
inputFileName = "Q-8271@gsa2.jobreport.txt" inputFileName = "Q-26618@gsa4.jobreport.txt"
#inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/Q-25718@node1149.jobreport.txt" #inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/Q-25718@node1149.jobreport.txt"
#inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/rodPerformanceGoals/history/report.082711.txt" #inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/rodPerformanceGoals/history/report.082711.txt"
outputPDF = NA outputPDF = NA
@ -129,9 +129,11 @@ plotGroup <- function(groupTable) {
# as above, but averaging over all iterations # as above, but averaging over all iterations
groupAnnotationsNoIteration = setdiff(groupAnnotations, "iteration") groupAnnotationsNoIteration = setdiff(groupAnnotations, "iteration")
if ( dim(sub)[1] > 1 ) { if ( dim(sub)[1] > 1 ) {
try({ # need a try here because we will fail to reduce when there's just a single iteration
sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd)) sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd))
textplot(as.data.frame(sum), show.rownames=F) textplot(as.data.frame(sum), show.rownames=F)
title(paste("Job summary for", name, "averaging over all iterations"), cex=3) title(paste("Job summary for", name, "averaging over all iterations"), cex=3)
}, silent=T)
} }
} }
@ -193,6 +195,7 @@ plotJobsGantt(gatkReportData, F, F)
plotProgressByTime(gatkReportData) plotProgressByTime(gatkReportData)
plotTimeByHost(gatkReportData) plotTimeByHost(gatkReportData)
for ( group in gatkReportData ) { for ( group in gatkReportData ) {
print(group)
plotGroup(group) plotGroup(group)
} }