{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/735","repository_url":"https://api.github.com/repos/bigdatagenomics/adam","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/735/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/735/comments","events_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/735/events","html_url":"https://github.com/bigdatagenomics/adam/issues/735","id":96589178,"number":735,"title":"adam2vcf fails with -coalesce","user":{"login":"antonstamov","id":6083971,"avatar_url":"https://avatars.githubusercontent.com/u/6083971?v=3","gravatar_id":"","url":"https://api.github.com/users/antonstamov","html_url":"https://github.com/antonstamov","followers_url":"https://api.github.com/users/antonstamov/followers","following_url":"https://api.github.com/users/antonstamov/following{/other_user}","gists_url":"https://api.github.com/users/antonstamov/gists{/gist_id}","starred_url":"https://api.github.com/users/antonstamov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antonstamov/subscriptions","organizations_url":"https://api.github.com/users/antonstamov/orgs","repos_url":"https://api.github.com/users/antonstamov/repos","events_url":"https://api.github.com/users/antonstamov/events{/privacy}","received_events_url":"https://api.github.com/users/antonstamov/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2015-07-22T15:02:21Z","updated_at":"2016-07-06T18:43:24Z","closed_at":"2016-07-06T18:43:24Z","body":"It fails with any coalesce value(1,4,10,etc)\r\n\r\nStacktrace:\r\n> org.apache.spark.SparkException: Job aborted due to stage failure: Task 3 in stage 41.0 failed 1 times, most recent failure: Lost task 3.0 in stage 41.0 (TID 333, localhost): com.esotericsoftware.kryo.KryoException: java.lang.NullPointerException\r\nSerialization trace:\r\nalleles (htsjdk.variant.variantcontext.FastGenotype)\r\ngenotypes (htsjdk.variant.variantcontext.VariantContext)\r\nvc (org.seqdoop.hadoop_bam.VariantContextWritable)\r\n\tat com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:626)\r\n\tat com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)\r\n\tat com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729)\r\n\tat com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:109)\r\n\tat com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:18)\r\n\tat com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)\r\n\tat com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)\r\n\tat com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)\r\n\tat com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)\r\n\tat com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)\r\n\tat com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)\r\n\tat com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729)\r\n\tat com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:42)\r\n\tat com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:33)\r\n\tat com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729)\r\n\tat org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:142)\r\n\tat org.apache.spark.serializer.DeserializationStream$$anon$1.getNext(Serializer.scala:133)\r\n\tat org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:71)\r\n\tat org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32)\r\n\tat scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)\r\n\tat org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32)\r\n\tat org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)\r\n\tat scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)\r\n\tat scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)\r\n\tat scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)\r\n\tat scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$12.apply(PairRDDFunctions.scala:987)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$12.apply(PairRDDFunctions.scala:965)\r\n\tat org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)\r\n\tat org.apache.spark.scheduler.Task.run(Task.scala:56)\r\n\tat org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:196)\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)\r\n\tat java.lang.Thread.run(Thread.java:745)\r\nCaused by: java.lang.NullPointerException\r\n\tat scala.collection.convert.Wrappers$MutableBufferWrapper.add(Wrappers.scala:80)\r\n\tat com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:109)\r\n\tat com.esotericsoftware.kryo.serializers.CollectionSerializer.read(CollectionSerializer.java:18)\r\n\tat com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)\r\n\tat com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)\r\n\t... 33 more"},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/comments/230866404","html_url":"https://github.com/bigdatagenomics/adam/issues/735#issuecomment-230866404","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/735","id":230866404,"user":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars.githubusercontent.com/u/3752466?v=3","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false},"created_at":"2016-07-06T18:43:24Z","updated_at":"2016-07-06T18:43:24Z","body":"Closing as not able to reproduce/issue is old."}}
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