java.lang.NoClassDefFoundError

org/apache/spark/Logging

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Solutions on the web19368

  • org/apache/spark/Logging
  • via GitHub by chetkhatri
    , 6 months ago
    org/apache/spark/Logging
  • Stack trace

    • java.lang.NoClassDefFoundError: org/apache/spark/Logging at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:763) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:467) at java.net.URLClassLoader.access$100(URLClassLoader.java:73) at java.net.URLClassLoader$1.run(URLClassLoader.java:368) at java.net.URLClassLoader$1.run(URLClassLoader.java:362) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:361) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at org.apache.spark.util.ChildFirstURLClassLoader.loadClass(MutableURLClassLoader.scala:52) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at org.bdgenomics.adam.serialization.ADAMKryoRegistrator.registerClasses(ADAMKryoRegistrator.scala:85) at org.broadinstitute.hellbender.engine.spark.GATKRegistrator.registerClasses(GATKRegistrator.java:74) at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$6.apply(KryoSerializer.scala:125) at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$6.apply(KryoSerializer.scala:125) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186) at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:125) at org.apache.spark.serializer.KryoSerializerInstance.borrowKryo(KryoSerializer.scala:274) at org.apache.spark.serializer.KryoSerializerInstance.<init>(KryoSerializer.scala:259) at org.apache.spark.serializer.KryoSerializer.newInstance(KryoSerializer.scala:175) at org.apache.spark.broadcast.TorrentBroadcast$.blockifyObject(TorrentBroadcast.scala:233) at org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:107) at org.apache.spark.broadcast.TorrentBroadcast.<init>(TorrentBroadcast.scala:86) at org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:34) at org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:56) at org.apache.spark.SparkContext.broadcast(SparkContext.scala:1370) at org.apache.spark.rdd.NewHadoopRDD.<init>(NewHadoopRDD.scala:76) at org.apache.spark.SparkContext$$anonfun$newAPIHadoopFile$2.apply(SparkContext.scala:1074) at org.apache.spark.SparkContext$$anonfun$newAPIHadoopFile$2.apply(SparkContext.scala:1065) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112) at org.apache.spark.SparkContext.withScope(SparkContext.scala:682) at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1065) at org.apache.spark.api.java.JavaSparkContext.newAPIHadoopFile(JavaSparkContext.scala:474) at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource.getParallelReads(ReadsSparkSource.java:104) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.getUnfilteredReads(GATKSparkTool.java:235) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.getReads(GATKSparkTool.java:209) at org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark.runTool(MarkDuplicatesSpark.java:65) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:348) at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:109) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:167) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:186) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:76) at org.broadinstitute.hellbender.Main.main(Main.java:92) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:729) at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:185) at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:210) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:124) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) Caused by: java.lang.ClassNotFoundException: org.apache.spark.Logging at java.lang.ClassLoader.findClass(ClassLoader.java:530) at org.apache.spark.util.ParentClassLoader.findClass(ParentClassLoader.scala:26) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at org.apache.spark.util.ParentClassLoader.loadClass(ParentClassLoader.scala:34) at org.apache.spark.util.ChildFirstURLClassLoader.loadClass(MutableURLClassLoader.scala:55) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 56 more

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