# Error split multiallelic **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [October 1, 2020, 7:14am UTC](https://discuss.hail.is/t/error-split-multiallelic/1719 "2020-10-01T07:14:36Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Santiago](https://avatars.discourse-cdn.com/v4/letter/s/3bc359/32.png) [@Santiago](https://discuss.hail.is/u/Santiago)\ **Post date:** [October 1, 2020, 7:14am UTC](https://discuss.hail.is/t/error-split-multiallelic/1719/1 "2020-10-01T07:14:36Z")
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) ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [October 1, 2020, 11:28am UTC](https://discuss.hail.is/t/error-split-multiallelic/1719/2 "2020-10-01T11:28:33Z")
Hi! This error is almost always caused by splitting a dataset that already has some split alleles. Do you call split multi hts twice? Is your input dataset already split? Try filtering to the locus printed in the error message and verify your input dataset has exactly one row, not two. ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [March 22, 2021, 4:32pm UTC](https://discuss.hail.is/t/error-split-multiallelic/1719/3 "2021-03-22T16:32:54Z")
2 posts were split to a new topic: [When running split\_multi\_hts, I received a key out of order error. Why do I receive that and what should I do?](https://discuss.hail.is/t/when-running-split-multi-hts-i-received-a-key-out-of-order-error-why-do-i-receive-that-and-what-should-i-do/1978)