java.lang.NoClassDefFoundError: org/apache/commons/compress/utils/CountingOutputStream

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,
Expert tip

A few things cause this exception:
1) Check if you have all jars and if they're in the correct path.
2) Your classpath might be broken, you can define it in the command line with java -cp yourClassPath or at your IDE if you're using one.

,

you can change your scala version to 2.11.11

Solutions on the web

via GitHub by akiezun
, 1 year ago
org/apache/commons/compress/utils/CountingOutputStream
via GitHub by antozito
, 1 year ago
org/apache/commons/compress/utils/CountingOutputStream
via GitHub by fleharty
, 2 years ago
org/apache/commons/compress/utils/CountingOutputStream
via GitHub by tinuthomas
, 1 year ago
org/apache/commons/compress/utils/CountingOutputStream
via GitHub by kaktus42
, 2 years ago
org/apache/commons/compress/utils/CountingOutputStream
java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at htsjdk.samtools.cram.build.CramIO.writeContainerForSamFileHeader(CramIO.java:269)
at htsjdk.samtools.cram.build.CramIO.writeCramHeader(CramIO.java:183)
at htsjdk.samtools.cram.build.CramIO.writeHeader(CramIO.java:118)
at htsjdk.samtools.CRAMContainerStreamWriter.writeHeader(CRAMContainerStreamWriter.java:116)
at htsjdk.samtools.CRAMFileWriter.writeHeader(CRAMFileWriter.java:119)
at htsjdk.samtools.SAMFileWriterImpl.setHeader(SAMFileWriterImpl.java:142)
at htsjdk.samtools.CRAMFileWriter.(CRAMFileWriter.java:105)
at htsjdk.samtools.SAMFileWriterFactory.createCRAMWriterWithSettings(SAMFileWriterFactory.java:485)
at htsjdk.samtools.SAMFileWriterFactory.makeCRAMWriter(SAMFileWriterFactory.java:435)
at htsjdk.samtools.SAMFileWriterFactory.makeWriter(SAMFileWriterFactory.java:381)
at picard.sam.RevertSam$RevertSamWriter.(RevertSam.java:556)
at picard.sam.RevertSam.doWork(RevertSam.java:222)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:100)
at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:48)
at picard.sam.RevertSamTest.testOutputByReadGroupWithOutputMap(RevertSamTest.java:172)
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.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:86)
at org.testng.internal.Invoker.invokeMethod(Invoker.java:643)
at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:820)
at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1128)
at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129)
at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
at org.testng.TestRunner.privateRun(TestRunner.java:782)
at org.testng.TestRunner.run(TestRunner.java:632)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:366)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319)
at org.testng.SuiteRunner.run(SuiteRunner.java:268)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1244)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1169)
at org.testng.TestNG.run(TestNG.java:1064)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:133)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:83)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
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.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.messaging.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)
at com.sun.proxy.$Proxy2.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:120)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at org.gradle.messaging.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:364)
at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

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