##### 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 Please 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 

##### ERROR

##### ERROR MESSAGE: An error occurred during the traversal.  Message=GC overhead limit exceeded

##### ERROR ------------------------------------------------------------------------------------------

finish at time 2012-10-22 21:02

问题产生原因：

根据sun的说法： "if too much time is being spent in garbage collection: if more than 98% of the total time is spent in garbage collection and less than 2% of the heap is recovered, an OutOfMemoryError will be thrown."

jvm gc行为中超过98%以上的时间去释放小于2%的堆空间时会报这个错误。

处理方法：

1. 在jvm启动参数中添加 "-XX:-UseGCOverheadLimit"，该参数在JDK6中默认启用("-XX:+UseGCOverheadLimit")。

　　调整后的生产环境中使用的参数为：　　　

JAVA_OPTS='-Xms512m -Xmx4096m -XX:MaxPermSize=128m -XX:-UseGCOverheadLimit -XX:+UseConcMarkSweepGC'

2. 检查是否有使用了大量内存的代码或死循环

3. 使用jstat命令监控gc行为是否正常

　　jstat监控gc的命令格式为：

　　jstat -gcutil [-t] [-h] [ []]　

　　vmid为JVM进程id，可以用ps -ef 或 jps -lv命令查找。

　　以下命令为每1秒钟输出一次gc状态，共输入5次

  S0     S1     E      O      P     YGC     YGCT    FGC    FGCT     GCT     0.00  93.34  85.63  82.95  59.73   1085   33.351    58    4.396   37.748 98.42   0.00  31.89  83.52  59.73   1088   33.487    58    4.396   37.883100.00  85.65 100.00  84.08  59.73   1091   33.554    58    4.396   37.950  0.00 100.00  54.30  84.49  59.73   1093   33.660    58    4.396   38.057 98.25   0.00  10.46  85.11  59.73   1096   33.768    58    4.396   38.164

　　经过一段时间的观察,确认是否正确