Re: NoClassDefFoundError: scala/Product$class
The org.bdgenomics.adam is one of the Components of the GATK, and I just download the release version from its github website . However, when I build a new docker image with spark2.4.5 and scala 2.12.4,It works well and that makes me confused. root@master2:~# pyspark Python 2.7.17 (default, Apr 15 2020, 17:20:14) [GCC 7.5.0] on linux2 Type "help", "copyright", "credits" or "license" for more information. 20/06/08 01:44:16 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties Setting default log level to "WARN". To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel). Welcome to __ / __/__ ___ _/ /__ _\ \/ _ \/ _ `/ __/ '_/ /__ / .__/\_,_/_/ /_/\_\ version 2.4.5 /_/ Using Python version 2.7.17 (default, Apr 15 2020 17:20:14) SparkSession available as 'spark'. root@master2:~# scala -version Scala code runner version 2.12.4 -- Copyright 2002-2017, LAMP/EPFL and Lightbend, Inc. -- Sent from: http://apache-spark-user-list.1001560.n3.nabble.com/ - To unsubscribe e-mail: user-unsubscr...@spark.apache.org
Re: NoClassDefFoundError: scala/Product$class
How are you depending on that org.bdgenomics.adam library? Maybe you're pulling the 2.11 version of that.
Re: NoClassDefFoundError: scala/Product$class
Spark 3 supports only Scala 2.12. This actually sounds like third party library is compiled for 2.11 or something. On Fri, Jun 5, 2020 at 11:11 PM charles_cai <1620075...@qq.com> wrote: > Hi Pol, > > thanks for your suggestion, I am going to use Spark-3.0.0 for GPU > acceleration,so I update the scala to the *version 2.12.11* and the latest > *2.13* ,but the error is still there, and by the way , the Spark version is > *spark-3.0.0-preview2-bin-without-hadoop* > > Caused by: java.lang.ClassNotFoundException: scala.Product$class > at java.net.URLClassLoader.findClass(URLClassLoader.java:382) > at java.lang.ClassLoader.loadClass(ClassLoader.java:418) > at java.lang.ClassLoader.loadClass(ClassLoader.java:351) > > Charles cai > > > > -- > Sent from: http://apache-spark-user-list.1001560.n3.nabble.com/ > > - > To unsubscribe e-mail: user-unsubscr...@spark.apache.org > >
Re: NoClassDefFoundError: scala/Product$class
Hi Pol, thanks for your suggestion, I am going to use Spark-3.0.0 for GPU acceleration,so I update the scala to the *version 2.12.11* and the latest *2.13* ,but the error is still there, and by the way , the Spark version is *spark-3.0.0-preview2-bin-without-hadoop* Caused by: java.lang.ClassNotFoundException: scala.Product$class at java.net.URLClassLoader.findClass(URLClassLoader.java:382) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) Charles cai -- Sent from: http://apache-spark-user-list.1001560.n3.nabble.com/ - To unsubscribe e-mail: user-unsubscr...@spark.apache.org
Re: NoClassDefFoundError: scala/Product$class
Hi Charles, I believe Spark 3.0 removed the support for Scala 2.11, and that error is a version compatibility issue. You should try Spark 2.4.5 with your current setup (works with Scala 2.11 by default). Pol Santamaria On Wed, Jun 3, 2020 at 7:44 AM charles_cai <1620075...@qq.com> wrote: > Hi, > > I run the GATK MarkDuplicates in Spark mode and it throws an > *NoClassDefFoundError: scala/Product$class*. The GATK version is 4.1.7 and > 4.0.0,the environment is: spark-3.0.0, scala-2.11.12 > > *GATK commands:* > > gatk MarkDuplicatesSpark \ > -I hdfs://master2:9000/Drosophila/output/Drosophila.sorted.bam \ > -O hdfs://master2:9000/Drosophila/output/Drosophila.sorted.markdup.bam \ > -M > hdfs://master2:9000/Drosophila/output/Drosophila.sorted.markdup_metrics.txt > \ > -- \ > --spark-runner SPARK --spark-master spark://master2:7077 > > *error logs:* > > Exception in thread "main" java.lang.NoClassDefFoundError: > scala/Product$class >at > org.bdgenomics.adam.serialization.InputStreamWithDecoder.(ADAMKryoRegistrator.scala:35) > >at > org.bdgenomics.adam.serialization.AvroSerializer.(ADAMKryoRegistrator.scala:45) > >at > org.bdgenomics.adam.models.VariantContextSerializer.(VariantContext.scala:94) > >at > org.bdgenomics.adam.serialization.ADAMKryoRegistrator.registerClasses(ADAMKryoRegistrator.scala:179) > >at > org.broadinstitute.hellbender.engine.spark.GATKRegistrator.registerClasses(GATKRegistrator.java:78) > >at > org.apache.spark.serializer.KryoSerializer.$anonfun$newKryo$8(KryoSerializer.scala:170) > >at > org.apache.spark.serializer.KryoSerializer.$anonfun$newKryo$8$adapted(KryoSerializer.scala:170) > >at scala.Option.foreach(Option.scala:407) >at > org.apache.spark.serializer.KryoSerializer.$anonfun$newKryo$5(KryoSerializer.scala:170) > >at > scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23) >at > org.apache.spark.util.Utils$.withContextClassLoader(Utils.scala:221) >at > org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:161) > >at > org.apache.spark.serializer.KryoSerializer$$anon$1.create(KryoSerializer.scala:102) > >at > com.esotericsoftware.kryo.pool.KryoPoolQueueImpl.borrow(KryoPoolQueueImpl.java:48) > >at > org.apache.spark.serializer.KryoSerializer$PoolWrapper.borrow(KryoSerializer.scala:109) > >at > org.apache.spark.serializer.KryoSerializerInstance.borrowKryo(KryoSerializer.scala:336) > >at > org.apache.spark.serializer.KryoSerializationStream.(KryoSerializer.scala:256) > >at > org.apache.spark.serializer.KryoSerializerInstance.serializeStream(KryoSerializer.scala:422) > >at > org.apache.spark.broadcast.TorrentBroadcast$.blockifyObject(TorrentBroadcast.scala:309) > >at > org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:137) > >at > org.apache.spark.broadcast.TorrentBroadcast.(TorrentBroadcast.scala:91) > >at > org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:35) > >at > org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:77) > >at org.apache.spark.SparkContext.broadcast(SparkContext.scala:1494) >at org.apache.spark.rdd.NewHadoopRDD.(NewHadoopRDD.scala:80) >at > org.apache.spark.SparkContext.$anonfun$newAPIHadoopFile$2(SparkContext.scala:1235) > >at > org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) > >at > org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) > >at org.apache.spark.SparkContext.withScope(SparkContext.scala:771) >at > org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1221) >at > org.apache.spark.api.java.JavaSparkContext.newAPIHadoopFile(JavaSparkContext.scala:484) > >at > > org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource.getParallelReads(ReadsSparkSource > .java:112) >at > org.broadinstitute.hellbender.engine.spark.GATKSparkTool.getUnfilteredReads(GATKSparkTool.java:254) > >at > org.broadinstitute.hellbender.engine.spark.GATKSparkTool.getReads(GATKSparkTool.java:220) > >at > > org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark.runTool(MarkDupli > catesSpark.java:72) >at > org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:387) > >at > > org.broadinstitute.hellbender.engine.spark.SparkC
NoClassDefFoundError: scala/Product$class
Hi, I run the GATK MarkDuplicates in Spark mode and it throws an *NoClassDefFoundError: scala/Product$class*. The GATK version is 4.1.7 and 4.0.0,the environment is: spark-3.0.0, scala-2.11.12 *GATK commands:* gatk MarkDuplicatesSpark \ -I hdfs://master2:9000/Drosophila/output/Drosophila.sorted.bam \ -O hdfs://master2:9000/Drosophila/output/Drosophila.sorted.markdup.bam \ -M hdfs://master2:9000/Drosophila/output/Drosophila.sorted.markdup_metrics.txt \ -- \ --spark-runner SPARK --spark-master spark://master2:7077 *error logs:* Exception in thread "main" java.lang.NoClassDefFoundError: scala/Product$class at org.bdgenomics.adam.serialization.InputStreamWithDecoder.(ADAMKryoRegistrator.scala:35) at org.bdgenomics.adam.serialization.AvroSerializer.(ADAMKryoRegistrator.scala:45) at org.bdgenomics.adam.models.VariantContextSerializer.(VariantContext.scala:94) at org.bdgenomics.adam.serialization.ADAMKryoRegistrator.registerClasses(ADAMKryoRegistrator.scala:179) at org.broadinstitute.hellbender.engine.spark.GATKRegistrator.registerClasses(GATKRegistrator.java:78) at org.apache.spark.serializer.KryoSerializer.$anonfun$newKryo$8(KryoSerializer.scala:170) at org.apache.spark.serializer.KryoSerializer.$anonfun$newKryo$8$adapted(KryoSerializer.scala:170) at scala.Option.foreach(Option.scala:407) at org.apache.spark.serializer.KryoSerializer.$anonfun$newKryo$5(KryoSerializer.scala:170) at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23) at org.apache.spark.util.Utils$.withContextClassLoader(Utils.scala:221) at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:161) at org.apache.spark.serializer.KryoSerializer$$anon$1.create(KryoSerializer.scala:102) at com.esotericsoftware.kryo.pool.KryoPoolQueueImpl.borrow(KryoPoolQueueImpl.java:48) at org.apache.spark.serializer.KryoSerializer$PoolWrapper.borrow(KryoSerializer.scala:109) at org.apache.spark.serializer.KryoSerializerInstance.borrowKryo(KryoSerializer.scala:336) at org.apache.spark.serializer.KryoSerializationStream.(KryoSerializer.scala:256) at org.apache.spark.serializer.KryoSerializerInstance.serializeStream(KryoSerializer.scala:422) at org.apache.spark.broadcast.TorrentBroadcast$.blockifyObject(TorrentBroadcast.scala:309) at org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:137) at org.apache.spark.broadcast.TorrentBroadcast.(TorrentBroadcast.scala:91) at org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:35) at org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:77) at org.apache.spark.SparkContext.broadcast(SparkContext.scala:1494) at org.apache.spark.rdd.NewHadoopRDD.(NewHadoopRDD.scala:80) at org.apache.spark.SparkContext.$anonfun$newAPIHadoopFile$2(SparkContext.scala:1235) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.SparkContext.withScope(SparkContext.scala:771) at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1221) at org.apache.spark.api.java.JavaSparkContext.newAPIHadoopFile(JavaSparkContext.scala:484) at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource.getParallelReads(ReadsSparkSource .java:112) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.getUnfilteredReads(GATKSparkTool.java:254) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.getReads(GATKSparkTool.java:220) at org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark.runTool(MarkDupli catesSpark.java:72) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:387) at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:30 ) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.jav a:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:152) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195) at org.broadinstitute.hellbender.Main.main(Main.java:275) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso