When I run sample_qc on phase 3 of the 1kgenome project I get an error saying " found non-biallelic variant: locus 1:15274, alleles A, G, T " . However, when I run the same code with phase 1, I do not get the error. What am I doing wrong?
The Phase 3 file I am using is “ALL.chr.phase3_shapeit2_mvncall_integrated_v2.20130502.genotypes.mt”
The error is as follows:
FatalError: HailException: in sample_qc: found non-biallelic variant: locus 1:15274, alleles A, G, T
Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 59.0 failed 4 times, most recent failure: Lost task 0.3 in stage 59.0 (TID 6203, hail103-w-0.c.avl-hail-ines.internal, executor 1): is.hail.utils.HailException: in sample_qc: found non-biallelic variant: locus 1:15274, alleles A, G, T
at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:9)
at is.hail.utils.package$.fatal(package.scala:26)
at is.hail.methods.VerifyBiallelic$$anonfun$apply$1.apply(VerifyBiallelic.scala:26)
at is.hail.methods.VerifyBiallelic$$anonfun$apply$1.apply(VerifyBiallelic.scala:15)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.next(Iterator.scala:444)
at is.hail.rvd.OrderedRVD$$anonfun$apply$19$$anon$3.next(OrderedRVD.scala:981)
at is.hail.rvd.OrderedRVD$$anonfun$apply$19$$anon$3.next(OrderedRVD.scala:975)
at scala.collection.Iterator$$anon$12.next(Iterator.scala:444)
at scala.collection.Iterator$class.foreach(Iterator.scala:893)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
at is.hail.methods.SampleQC$$anonfun$results$1.apply(SampleQC.scala:175)
at is.hail.methods.SampleQC$$anonfun$results$1.apply(SampleQC.scala:170)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$18.apply(ContextRDD.scala:291)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$18.apply(ContextRDD.scala:291)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$18$$anonfun$apply$19.apply(ContextRDD.scala:291)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$18$$anonfun$apply$19.apply(ContextRDD.scala:291)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:438)
at org.apache.spark.rdd.RDD$$anonfun$treeReduce$1$$anonfun$17.apply(RDD.scala:1041)
at org.apache.spark.rdd.RDD$$anonfun$treeReduce$1$$anonfun$17.apply(RDD.scala:1040)
at org.apache.spark.rdd.RDD$$anonfun$treeReduce$1$$anonfun$18.apply(RDD.scala:1047)
at org.apache.spark.rdd.RDD$$anonfun$treeReduce$1$$anonfun$18.apply(RDD.scala:1047)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1517)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1505)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1504)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1504)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1732)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1687)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1676)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2029)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126)
at org.apache.spark.rdd.RDD$$anonfun$reduce$1.apply(RDD.scala:1026)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.RDD.reduce(RDD.scala:1008)
at org.apache.spark.rdd.RDD$$anonfun$treeAggregate$1.apply(RDD.scala:1151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.RDD.treeAggregate(RDD.scala:1128)
at org.apache.spark.rdd.RDD$$anonfun$treeReduce$1.apply(RDD.scala:1059)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.RDD.treeReduce(RDD.scala:1037)
at is.hail.methods.SampleQC$.results(SampleQC.scala:207)
at is.hail.methods.SampleQC$.apply(SampleQC.scala:222)
at is.hail.methods.SampleQC.apply(SampleQC.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:280)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:214)
at java.lang.Thread.run(Thread.java:748)is.hail.utils.HailException: in sample_qc: found non-biallelic variant: locus 1:15274, alleles A, G, T
at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:9)
at is.hail.utils.package$.fatal(package.scala:26)
at is.hail.methods.VerifyBiallelic$$anonfun$apply$1.apply(VerifyBiallelic.scala:26)
at is.hail.methods.VerifyBiallelic$$anonfun$apply$1.apply(VerifyBiallelic.scala:15)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.next(Iterator.scala:444)
at is.hail.rvd.OrderedRVD$$anonfun$apply$19$$anon$3.next(OrderedRVD.scala:981)
at is.hail.rvd.OrderedRVD$$anonfun$apply$19$$anon$3.next(OrderedRVD.scala:975)
at scala.collection.Iterator$$anon$12.next(Iterator.scala:444)
at scala.collection.Iterator$class.foreach(Iterator.scala:893)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
at is.hail.methods.SampleQC$$anonfun$results$1.apply(SampleQC.scala:175)
at is.hail.methods.SampleQC$$anonfun$results$1.apply(SampleQC.scala:170)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$18.apply(ContextRDD.scala:291)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$18.apply(ContextRDD.scala:291)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$18$$anonfun$apply$19.apply(ContextRDD.scala:291)
at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitions$1$$anonfun$apply$18$$anonfun$apply$19.apply(ContextRDD.scala:291)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:438)
at org.apache.spark.rdd.RDD$$anonfun$treeReduce$1$$anonfun$17.apply(RDD.scala:1041)
at org.apache.spark.rdd.RDD$$anonfun$treeReduce$1$$anonfun$17.apply(RDD.scala:1040)
at org.apache.spark.rdd.RDD$$anonfun$treeReduce$1$$anonfun$18.apply(RDD.scala:1047)
at org.apache.spark.rdd.RDD$$anonfun$treeReduce$1$$anonfun$18.apply(RDD.scala:1047)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338)
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)
Hail version: devel-56ea3941ae61
Error summary: HailException: in sample_qc: found non-biallelic variant: locus 1:15274, alleles A, G, T