java.lang.AssertionError: line counts expected [2629] but found [507]

GitHub | cmnbroad | 3 months ago
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  1. 0

    GitHub comment 835#268623874

    GitHub | 4 months ago | droazen
    java.lang.AssertionError: Line number 109 (not counting comments) expected [20 10012362 . G T 835.77 . AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=3200.000;MLEAC=2;MLEAF=1.00;QD=35.92;RAW_MQ=66527.00;SOR=4.003 GT:AD:DP:GQ:PL 1/1:0,23:23:69:864,69,0] but found [20 10012362 . G T 835.77 . AC=2;AF=1.00;AN=2;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=35.92;RAW_MQ=66527.00;SOR=4.003 GT:AD:DP:GQ:PL 1/1:0,23:23:69:864,69,0]
  2. 0

    ExampleAssemblyRegionWalkerSparkIntegrationTest fails intermittently

    GitHub | 3 months ago | cmnbroad
    java.lang.AssertionError: line counts expected [2629] but found [507]
  3. 0

    PCAUnitTest.testSparkSVDOnTestMatrix failing intermittently on travis.

    GitHub | 1 year ago | samuelklee
    java.lang.AssertionError: expected [4] but found [3]
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Root Cause Analysis

  1. java.lang.AssertionError

    line counts expected [2629] but found [507]

    at org.testng.Assert.fail()
  2. TestNG
    Assert.assertEquals
    1. org.testng.Assert.fail(Assert.java:94)
    2. org.testng.Assert.failNotEquals(Assert.java:496)
    3. org.testng.Assert.assertEquals(Assert.java:125)
    4. org.testng.Assert.assertEquals(Assert.java:372)
    4 frames
  3. org.broadinstitute.hellbender
    ExampleAssemblyRegionWalkerSparkIntegrationTest.testExampleAssemblyRegionWalker
    1. org.broadinstitute.hellbender.utils.test.IntegrationTestSpec.assertEqualTextFiles(IntegrationTestSpec.java:211)
    2. org.broadinstitute.hellbender.utils.test.IntegrationTestSpec.assertEqualTextFiles(IntegrationTestSpec.java:190)
    3. org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSparkIntegrationTest.testExampleAssemblyRegionWalker(ExampleAssemblyRegionWalkerSparkIntegrationTest.java:29)
    3 frames
  4. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    4. java.lang.reflect.Method.invoke(Method.java:498)
    4 frames
  5. TestNG
    TestNG.run
    1. org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
    2. org.testng.internal.Invoker.invokeMethod(Invoker.java:639)
    3. org.testng.internal.Invoker.invokeTestMethod(Invoker.java:821)
    4. org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1131)
    5. org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
    6. org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
    7. org.testng.TestRunner.privateRun(TestRunner.java:773)
    8. org.testng.TestRunner.run(TestRunner.java:623)
    9. org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
    10. org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
    11. org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
    12. org.testng.SuiteRunner.run(SuiteRunner.java:259)
    13. org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
    14. org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
    15. org.testng.TestNG.runSuitesSequentially(TestNG.java:1185)
    16. org.testng.TestNG.runSuitesLocally(TestNG.java:1110)
    17. org.testng.TestNG.run(TestNG.java:1018)
    17 frames
  6. org.gradle.api
    SuiteTestClassProcessor.stop
    1. org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129)
    2. org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88)
    3. org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
    3 frames
  7. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    4. java.lang.reflect.Method.invoke(Method.java:498)
    4 frames
  8. org.gradle.internal
    ProxyDispatchAdapter$DispatchingInvocationHandler.invoke
    1. org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
    2. org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
    3. org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)
    4. org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)
    4 frames
  9. com.sun.proxy
    $Proxy2.stop
    1. com.sun.proxy.$Proxy2.stop(Unknown Source)
    1 frame
  10. org.gradle.api
    TestWorker.stop
    1. org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:120)
    1 frame
  11. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    4. java.lang.reflect.Method.invoke(Method.java:498)
    4 frames
  12. org.gradle.internal
    MessageHub$Handler.run
    1. org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
    2. org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
    3. org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:377)
    3 frames
  13. Gradle Core
    StoppableExecutorImpl$1.run
    1. org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
    2. org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
    2 frames
  14. Java RT
    Thread.run
    1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    3. java.lang.Thread.run(Thread.java:745)
    3 frames