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ReadsPipelineSpark fails on a cluster with KryoException #6091

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tomwhite opened this issue Aug 13, 2019 · 1 comment · Fixed by #6094
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ReadsPipelineSpark fails on a cluster with KryoException #6091

tomwhite opened this issue Aug 13, 2019 · 1 comment · Fixed by #6094
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@tomwhite
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@tomwhite
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Running scripts/spark_wdl fails with:

com.esotericsoftware.kryo.KryoException: java.lang.RuntimeException: Could not serialize lambda
Serialization trace:
initializer (htsjdk.samtools.util.Lazy)
dictionary (htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile)
sequenceFile (org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile)
val$taskReferenceSequenceFile (org.broadinstitute.hellbender.tools.HaplotypeCallerSpark$1)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:101)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:518)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:552)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:80)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:518)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:552)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:80)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:518)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:552)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:80)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:518)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:628)
	at org.apache.spark.serializer.KryoSerializationStream.writeObject(KryoSerializer.scala:241)
	at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$blockifyObject$2.apply(TorrentBroadcast.scala:291)
	at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$blockifyObject$2.apply(TorrentBroadcast.scala:291)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1381)
	at org.apache.spark.broadcast.TorrentBroadcast$.blockifyObject(TorrentBroadcast.scala:292)
	at org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:127)
	at org.apache.spark.broadcast.TorrentBroadcast.<init>(TorrentBroadcast.scala:88)
	at org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:34)
	at org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:62)
	at org.apache.spark.SparkContext.broadcast(SparkContext.scala:1482)
	at org.apache.spark.api.java.JavaSparkContext.broadcast(JavaSparkContext.scala:650)
	at org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.assemblyRegionEvaluatorSupplierBroadcastFunction(HaplotypeCallerSpark.java:265)
	at org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.assemblyRegionEvaluatorSupplierBroadcast(HaplotypeCallerSpark.java:245)
	at org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.callVariantsWithHaplotypeCallerAndWriteOutput(HaplotypeCallerSpark.java:303)
	at org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark.runTool(ReadsPipelineSpark.java:224)
	at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533)
	at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
	at org.broadinstitute.hellbender.Main.main(Main.java:291)
	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 org.apache.spark.deploy.JavaMainApplication.start(SparkApplication.scala:52)
	at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:894)
	at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:198)
	at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:228)
	at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:137)
	at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.RuntimeException: Could not serialize lambda
	at com.twitter.chill.java.ClosureSerializer.write(ClosureSerializer.java:70)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:552)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:80)
	... 44 more
Caused by: java.lang.NoSuchMethodException: htsjdk.samtools.reference.AbstractFastaSequenceFile$$Lambda$94/1029586776.writeReplace()
	at java.lang.Class.getDeclaredMethod(Class.java:2130)
	at com.twitter.chill.java.ClosureSerializer.write(ClosureSerializer.java:61)
	... 46 more
@tomwhite tomwhite added the Spark label Aug 13, 2019
@tomwhite tomwhite self-assigned this Aug 13, 2019
@tomwhite tomwhite mentioned this issue Aug 13, 2019
Merged
lbergelson added a commit that referenced this issue Aug 14, 2019
@lbergelson
Update htsjdk to 2.20.2
d5dc015 
* Update htsjdk 2.20.1 -> 2.20.2
* This release fixes #6091
@lbergelson lbergelson mentioned this issue Aug 14, 2019
Merged
lbergelson added a commit that referenced this issue Aug 14, 2019
@lbergelson
Update htsjdk to 2.20.2
38f98a0 
* Update htsjdk 2.20.1 -> 2.20.2
* This release fixes #6091
lbergelson added a commit that referenced this issue Aug 15, 2019
@lbergelson
Update htsjdk to 2.20.2 (#6094)
69391bf 
* Update htsjdk 2.20.1 -> 2.20.2
* This fixes #6091
@cmnbroad
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cmnbroad commented Oct 2, 2019

Looks like another user hit this issue.

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Update htsjdk to 2.20.2 broadinstitute/gatk
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