##### ERROR Stack Trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException:An error occurred during the traversal. MESSAGE=GC overhead limit exceeded
At Org.broadinstitute.sting.gatk.executive.HierarchicalMicroSchedulEr.toruntimeexception (Hierarchicalmicroscheduler.java:368)
At Org.broadinstitute.sting.gatk.executive.HierarchicalMicroSchedulEr.notifyoftraversalerror (Hierarchicalmicroscheduler.java:359)
At Org.broadinstitute.sting.gatk.executive.ShardTraverser.call (shardtraverser.java:84)
At Java.util.concurrent.futuretask$sync.innerrun (futuretask.java:334)
At Java.util.concurrent.FutureTask.run (futuretask.java:166)
At Java.util.concurrent.ThreadPoolExecutor.runWorker (threadpoolexecutor.java:1110)
At Java.util.concurrent.threadpoolexecutor$worker.run (threadpoolexecutor.java:603)
At Java.lang.Thread.run (thread.java:722)
caused By:java.lang.OutOfMemoryError:GC overhead limit exceeded
At Org.broadinstitute.sting.gatk.walkers.genotyper.AlleleFrequencyCalculatiOnmodel$exactacset. (Allelefrequencycalculationmodel.java:190)
At Org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.updateACset ( exactafcalculationmodel.java:242)
At org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.calculateAlleleCountConfOrmation (exactafcalculationmodel.java:225)
At Org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.linearExactMultiAllelic ( exactafcalculationmodel.java:139)
At Org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.getLog10PNonRef ( EXACTAFCALCULATIONMODEL.JAVA:64)
At Org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateGenotypes ( unifiedgenotyperengine.java:470)
At Org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGEnotypes (unifiedgenotyperengine.java:192)
At Org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map (unifiedgenotyper.java:353)
At Org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map (unifiedgenotyper.java:119)
At Org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse (traverseloci.java:65)
At Org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse (traverseloci.java:18)
At Org.broadinstitute.sting.gatk.executive.ShardTraverser.call (shardtraverser.java:70)
... 5 more
##### ERROR------------------------------------------------------------------------------------------
##### Error A GATK RUNTIME error has occurred (version 2.0-35-gb3e7fbe):
##### ERROR
##### ERROR Visit the wiki to see if this is a known problem
##### error If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit Our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### Error Message:an error occurred during the traversal.MESSAGE=GC Overhead limit exceeded
##### ERROR------------------------------------------------------------------------------------------
Finish at time 2012-10-22 21:02
The cause of the problem arises:
According to Sun, "if too much time is being spent in garbage collection:if more than 98% of the total time was spent in garbage c Ollection and less than 2% of the heap are recovered, an outofmemoryerror would be thrown. "
This error is reported when the JVM GC behaves more than 98% of the time to release less than 2% of the heap space.
Processing method:
1. Add "-xx:-usegcoverheadlimit" to the JVM startup parameter, which is enabled by default ("-xx:+usegcoverheadlimit") in JDK6.
The parameters used in the adjusted production environment are:
java_opts='-xms512m-xmx4096m-xx:maxpermsize=128m -xx:-usegcoverheadlimit-xx:+ USECONCMARKSWEEPGC'
2. Check for code that uses a lot of memory or a dead loop
3. Use the Jstat command to monitor whether GC behavior is normal
The command format for the JSTAT monitoring GC is:
Jstat-gcutil [-T] [-h] [[]]
Vmid is the JVM process ID and can be found with the PS-EF or JPS-LV command.
The following command outputs GC status every 1 seconds, with a total of 5 inputs
S0S1E OPYgcYgctFGCFgctGCT0.0093.3485.6382.9559.73108533.351584.39637.74898.420.0031.8983.5259.73108833.487584.39637.883100.0085.65 100.0084.0859.73109133.554584.39637.9500.00 100.0054.3084.4959.73109333.660584.39638.05798.250.0010.4685.1159.73109633.768584.39638.164
After a period of observation, confirm whether it is correct
Android GC overhead limit exceeded
