From ff61aeb76239d884d73cabb5f937efbefd8d3aeb Mon Sep 17 00:00:00 2001 From: depristo Date: Sat, 22 Jan 2011 15:02:02 +0000 Subject: [PATCH] continuing to push to get right answers for long-running jobs git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5054 348d0f76-0448-11de-a6fe-93d51630548a --- analysis/depristo/distributedGATK/distributedGATKMetrics.py | 2 ++ analysis/depristo/distributedGATK/runqueue.csh | 3 ++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/analysis/depristo/distributedGATK/distributedGATKMetrics.py b/analysis/depristo/distributedGATK/distributedGATKMetrics.py index c7d50d59e..ed8beedec 100755 --- a/analysis/depristo/distributedGATK/distributedGATKMetrics.py +++ b/analysis/depristo/distributedGATK/distributedGATKMetrics.py @@ -32,6 +32,8 @@ def main(): print file, dataset, parallelType, nWays, formatTime(startTime), formatTime(endTime), endToEnd(endTime, startTime), perMSites, runtime def endToEnd(endTime, startTime): + if endTime < startTime: + endTime = endTime + datetime.timedelta(1) #print 'endToEnd', endTime, startTime return total_minutes(endTime - startTime) diff --git a/analysis/depristo/distributedGATK/runqueue.csh b/analysis/depristo/distributedGATK/runqueue.csh index 7ace30a15..78539cb81 100755 --- a/analysis/depristo/distributedGATK/runqueue.csh +++ b/analysis/depristo/distributedGATK/runqueue.csh @@ -1,9 +1,10 @@ #!/bin/tcsh -setenv CMD "java -Djava.io.tmpdir=/broad/shptmp/depristo/tmp -jar /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/dist/Queue.jar -statusTo depristo -S /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/scala/qscript/oneoffs/depristo/distributedGATKPerformance.scala -bsub --gatkjarfile /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/dist/GenomeAnalysisTK.jar -dataset HiSeq $argv[2-$#argv]" +setenv CMD "java -Djava.io.tmpdir=/broad/shptmp/depristo/tmp -jar /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/dist/Queue.jar -statusTo depristo -S /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/analysis/depristo/distributedGATK/distributedGATKPerformance.scala -bsub --gatkjarfile /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/dist/GenomeAnalysisTK.jar -dataset HiSeq $argv[2-$#argv]" if ( $1 == 1 ) then pushd short; $CMD -jobQueue hour -run & +else if ( $1 == 2 ) then pushd long; $CMD -jobQueue gsa -long -run & else $CMD