##### ERROR
------------------------------------------------------------------------------------------
##### 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 http://www./gatk
##### ERROR
##### ERROR MESSAGE: An error occurred during the
traversal. Message=GC overhead limit
exceeded
##### ERROR
------------------------------------------------------------------------------------------
finish at time 2012-10-22 21:02
問題產(chǎn)生原因：
根據(jù)sun的說法： "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行為中超過98%以上的時(shí)間去釋放小于2%的堆空間時(shí)會(huì)報(bào)這個(gè)錯(cuò)誤。
處理方法：
1. 在jvm啟動(dòng)參數(shù)中添加
"-XX:-UseGCOverheadLimit"，該參數(shù)在JDK6中默認(rèn)啟用("-XX:+UseGCOverheadLimit")。
調(diào)整后的生產(chǎn)環(huán)境中使用的參數(shù)為：
JAVA_OPTS='-Xms512m -Xmx4096m -XX:MaxPermSize=128m -XX:-UseGCOverheadLimit -XX:+UseConcMarkSweepGC'
2. 檢查是否有使用了大量內(nèi)存的代碼或死循環(huán)
3. 使用jstat命令監(jiān)控gc行為是否正常
jstat監(jiān)控gc的命令格式為：
jstat -gcutil [-t] [-h] [
[]]
vmid為JVM進(jìn)程id，可以用ps -ef 或 jps -lv命令查找。
以下命令為每1秒鐘輸出一次gc狀態(tài)，共輸入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 37.883
100.00 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
經(jīng)過一段時(shí)間的觀察,確認(rèn)是否正確
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