Hi,
when I split multiallelic variants I get an error in one case:
hail.utils.java.FatalError: HailException: RVD error! Keys found out of order:
Current key: { locus: { contig: chr3, position: 16902883 }, alleles: [2; N, GGGGTGCGC] }
Previous key: { locus: { contig: chr3, position: 16902883 }, alleles: [2; NGCGCAT, CGCGGGCCG] }
This error can occur after a split_multi if the dataset
contains both multiallelic variants and duplicated loci.
Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 227 in stage 6.0 failed 1 times, most recent failure: Lost task 227.0 in stage 6.0 (TID 3320, localhost, executor driver): is.hail.utils.HailException: RVD error! Keys found out of order:
Current key: { locus: { contig: chr3, position: 16902883 }, alleles: [2; N, GGGGTGCGC] }
Previous key: { locus: { contig: chr3, position: 16902883 }, alleles: [2; NGCGCAT, CGCGGGCCG] }
This error can occur after a split_multi if the dataset
contains both multiallelic variants and duplicated loci.
at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:9)
at is.hail.utils.package$.fatal(package.scala:77)
at is.hail.rvd.RVD$$anonfun$checkKeyOrdering$1$$anon$1.next(RVD.scala:224)
at is.hail.rvd.RVD$$anonfun$checkKeyOrdering$1$$anon$1.next(RVD.scala:208)
at scala.collection.Iterator$$anon$12.next(Iterator.scala:445)
at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.next(RichContextRDDRegionValue.scala:196)
at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.next(RichContextRDDRegionValue.scala:180)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:410)
at scala.collection.Iterator$$anon$12.next(Iterator.scala:445)
at scala.collection.Iterator$$anon$1.next(Iterator.scala:1008)
at scala.collection.Iterator$$anon$1.head(Iterator.scala:995)
at is.hail.utils.richUtils.RichIterator$$anon$5.value(RichIterator.scala:29)
at is.hail.utils.StagingIterator.consume(FlipbookIterator.scala:57)
at is.hail.utils.FlipbookIterator$MergeStateMachine$1.advance(FlipbookIterator.scala:451)
at is.hail.utils.StagingIterator.stage(FlipbookIterator.scala:61)
at is.hail.utils.StagingIterator.hasNext(FlipbookIterator.scala:71)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.io.RichContextRDDLong$$anonfun$boundary$extension$2$$anon$1.hasNext(RichContextRDDRegionValue.scala:188)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$1.hasNext(Iterator.scala:1002)
at is.hail.utils.richUtils.RichIterator$$anon$5.isValid(RichIterator.scala:30)
at is.hail.utils.StagingIterator.isValid(FlipbookIterator.scala:48)
at is.hail.utils.FlipbookIterator$$anon$9.setValue(FlipbookIterator.scala:327)
at is.hail.utils.FlipbookIterator$$anon$9.advance(FlipbookIterator.scala:341)
at is.hail.utils.StagingIterator.advance(FlipbookIterator.scala:53)
at is.hail.utils.FlipbookIterator$$anon$5.advance(FlipbookIterator.scala:179)
at is.hail.utils.StagingIterator.stage(FlipbookIterator.scala:61)
at is.hail.utils.StagingIterator.hasNext(FlipbookIterator.scala:71)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:66)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:221)
at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:121)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:403)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:409)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1889)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2158)
at is.hail.rvd.RVD.combine(RVD.scala:724)
at is.hail.expr.ir.Interpret$.run(Interpret.scala:941)
at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:53)
at is.hail.expr.ir.InterpretNonCompilable$.interpretAndCoerce$1(InterpretNonCompilable.scala:16)
at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:53)
at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:58)
at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.transform(LoweringPass.scala:67)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13)
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13)
at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:62)
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:14)
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:12)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:12)
at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:28)
at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:334)
at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:321)
at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:320)
at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:20)
at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:18)
at is.hail.utils.package$.using(package.scala:609)
at is.hail.annotations.Region$.scoped(Region.scala:18)
at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:18)
at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:230)
at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:320)
at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:349)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)