droazen
commented
7 years ago Issue moved to broadinstitute/gatk #3018 via ZenHub
Closed TianJin297 closed 7 years ago
droazen
commented
7 years ago Issue moved to broadinstitute/gatk #3018 via ZenHub
When I was running HaplotypeCallorSpark with one of my samples, I got an error as "Duplicate key".
The command I used is "/gatk-protected HaplotypeCallerSpark -I XX_BQSRappliedspark.bam -O XX_525.gvcf -R /curr/data/humann_g1k_v37.2bit --emitRefConfidence BP_RESOLUTION --TMP_DIR tmp"
And it runs on Amazon instance m4.2xlarge.
00:10:41.089 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 00:10:41.089 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 00:10:41.089 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 00:10:45.460 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 00:10:45.460 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null 00:11:09.609 WARN TaskMemoryManager:381 - leak 166.6 MB memory from org.apache.spark.util.collection.ExternalAppendOnlyMap@60a3c432 00:11:09.611 ERROR Executor:91 - Exception in task 15.0 in stage 1.0 (TID 519) java.lang.IllegalStateException: Duplicate key [B@4e233a3c at java.util.stream.Collectors.lambda$throwingMerger$0(Collectors.java:133) at java.util.HashMap.merge(HashMap.java:1253) at java.util.stream.Collectors.lambda$toMap$58(Collectors.java:1320) at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.buildGapContinuationPenalties(PairHMMLikelihoodCalculat ionEngine.java:304) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngi ne.java:253) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngi ne.java:187) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:518) at org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.lambda$regionToVariants$2(HaplotypeCallerSpark.java:192) at java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:267) at java.util.Spliterators$IteratorSpliterator.tryAdvance(Spliterators.java:1812) at java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294) at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206) at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:169) at java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300) at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681) at scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310) at scala.collection.AbstractIterator.to(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302) at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289) at scala.collection.AbstractIterator.toArray(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289) at scala.collection.AbstractIterator.toArray(Iterator.scala:1336) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:912) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:912) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1899) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1899) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70) at org.apache.spark.scheduler.Task.run(Task.scala:86) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:748) 00:11:09.632 WARN TaskSetManager:66 - Lost task 15.0 in stage 1.0 (TID 519, localhost): java.lang.IllegalStateException: Duplicate key [B@4e233a3c at java.util.stream.Collectors.lambda$throwingMerger$0(Collectors.java:133) at java.util.HashMap.merge(HashMap.java:1253) at java.util.stream.Collectors.lambda$toMap$58(Collectors.java:1320) at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.buildGapContinuationPenalties(PairHMMLikelihoodCalculat ionEngine.java:304) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngi ne.java:253) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngi ne.java:187) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:518) at org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.lambda$regionToVariants$2(HaplotypeCallerSpark.java:192) at java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:267) at java.util.Spliterators$IteratorSpliterator.tryAdvance(Spliterators.java:1812) at java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294) at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206) at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:169) at java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300) at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681) at scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310) at scala.collection.AbstractIterator.to(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302) at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289) at scala.collection.AbstractIterator.toArray(Iterator.scala:1336) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:912) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:912) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1899) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1899) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70) at org.apache.spark.scheduler.Task.run(Task.scala:86) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:748)
00:11:09.634 ERROR TaskSetManager:70 - Task 15 in stage 1.0 failed 1 times; aborting job 00:11:09.810 WARN TaskSetManager:66 - Lost task 33.0 in stage 1.0 (TID 528, localhost): TaskKilled (killed intentionally) 00:11:24.786 INFO HaplotypeCallerSpark - Shutting down engine [May 26, 2017 12:11:24 AM UTC] org.broadinstitute.hellbender.tools.HaplotypeCallerSpark done. Elapsed time: 10.58 minutes. Runtime.totalMemory()=16622026752 org.apache.spark.SparkException: Job aborted due to stage failure: Task 15 in stage 1.0 failed 1 times, most recent failure: Lost task 15.0 in stage 1.0 (TID 519 , localhost): java.lang.IllegalStateException: Duplicate key [B@4e233a3c at java.util.stream.Collectors.lambda$throwingMerger$0(Collectors.java:133) at java.util.HashMap.merge(HashMap.java:1253) at java.util.stream.Collectors.lambda$toMap$58(Collectors.java:1320) at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.buildGapContinuationPenalties(PairHMMLikelihoodCalculat ionEngine.java:304) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngi ne.java:253) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngi ne.java:187) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:518) at org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.lambda$regionToVariants$2(HaplotypeCallerSpark.java:192) at java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:267) at java.util.Spliterators$IteratorSpliterator.tryAdvance(Spliterators.java:1812) at java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294) at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206) at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:169) at java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300) at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681) at scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310) at scala.collection.AbstractIterator.to(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302) at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289) at scala.collection.AbstractIterator.toArray(Iterator.scala:1336) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:912) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:912) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1899) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1899) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70) at org.apache.spark.scheduler.Task.run(Task.scala:86) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:748)
Driver stacktrace: at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1454) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1442) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1441) at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48) at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1441) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:811) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:811) at scala.Option.foreach(Option.scala:257) at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:811) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1667) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1622) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1611) at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48) at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:632) at org.apache.spark.SparkContext.runJob(SparkContext.scala:1873) at org.apache.spark.SparkContext.runJob(SparkContext.scala:1886) at org.apache.spark.SparkContext.runJob(SparkContext.scala:1899) at org.apache.spark.SparkContext.runJob(SparkContext.scala:1913) at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:912) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.rdd.RDD.withScope(RDD.scala:358) at org.apache.spark.rdd.RDD.collect(RDD.scala:911) at org.apache.spark.api.java.JavaRDDLike$class.collect(JavaRDDLike.scala:360) at org.apache.spark.api.java.AbstractJavaRDDLike.collect(JavaRDDLike.scala:45) at org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.writeVariants(HaplotypeCallerSpark.java:205) at org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.runTool(HaplotypeCallerSpark.java:115) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:353) at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:116) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:121) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:142) at org.broadinstitute.hellbender.Main.main(Main.java:220) Caused by: java.lang.IllegalStateException: Duplicate key [B@4e233a3c at java.util.stream.Collectors.lambda$throwingMerger$0(Collectors.java:133) at java.util.HashMap.merge(HashMap.java:1253) at java.util.stream.Collectors.lambda$toMap$58(Collectors.java:1320) at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.buildGapContinuationPenalties(PairHMMLikelihoodCalculat ionEngine.java:304) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngi ne.java:253) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngi ne.java:187) at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:518) at org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.lambda$regionToVariants$2(HaplotypeCallerSpark.java:192) at java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:267) at java.util.Spliterators$IteratorSpliterator.tryAdvance(Spliterators.java:1812) at java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294) at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206) at java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:169) at java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300) at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681) at scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42) at scala.collection.Iterator$class.foreach(Iterator.scala:893) at scala.collection.AbstractIterator.foreach(Iterator.scala:1336) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310) at scala.collection.AbstractIterator.to(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302) at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289) at scala.collection.AbstractIterator.toArray(Iterator.scala:1336) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:912) at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:912) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1899) at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1899) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70) at org.apache.spark.scheduler.Task.run(Task.scala:86) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:748)