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  1. ,
    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.

  2. ,

    you can change your scala version to 2.11.11

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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 org.gradle.messaging.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)	at com.sun.proxy.$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.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)	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 org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)	at java.lang.Thread.run(Thread.java:745)