Class org.broadinstitute.hellbender.utils.io.IOUtilsUnitTest

all > org.broadinstitute.hellbender.utils.io > IOUtilsUnitTest

tests

failures

ignored

2.092s

duration

97%

successful

Failed tests
Tests
Standard error

Failed tests

testAppendPathToDir

org.apache.hadoop.ipc.RemoteException(java.lang.NoClassDefFoundError): Could not initialize class org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol.getDescriptor(ClientNamenodeProtocolProtos.java)
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.getDescriptorForType(ClientNamenodeProtocolProtos.java)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573)
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227)
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246)
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712)
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439)
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953)
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203)

	at app//org.apache.hadoop.ipc.Client.getRpcResponse(Client.java:1584)
	at app//org.apache.hadoop.ipc.Client.call(Client.java:1529)
	at app//org.apache.hadoop.ipc.Client.call(Client.java:1426)
	at app//org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:258)
	at app//org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:139)
	at app/jdk.proxy3/jdk.proxy3.$Proxy60.getDatanodeReport(Unknown Source)
	at app//org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.lambda$getDatanodeReport$28(ClientNamenodeProtocolTranslatorPB.java:713)
	at app//org.apache.hadoop.ipc.internal.ShadedProtobufHelper.ipc(ShadedProtobufHelper.java:160)
	at app//org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.getDatanodeReport(ClientNamenodeProtocolTranslatorPB.java:713)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:437)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeMethod(RetryInvocationHandler.java:170)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invoke(RetryInvocationHandler.java:162)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeOnce(RetryInvocationHandler.java:100)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:366)
	at app/jdk.proxy3/jdk.proxy3.$Proxy61.getDatanodeReport(Unknown Source)
	at app//org.apache.hadoop.hdfs.DFSClient.datanodeReport(DFSClient.java:2134)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2869)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2920)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.startDataNodes(MiniDFSCluster.java:1848)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.initMiniDFSCluster(MiniDFSCluster.java:995)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.<init>(MiniDFSCluster.java:594)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster$Builder.build(MiniDFSCluster.java:533)
	at app//org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:30)
	at app//org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:38)
	at app//org.broadinstitute.hellbender.utils.io.IOUtilsUnitTest.testAppendPathToDir(IOUtilsUnitTest.java:476)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568)
	at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511)
	at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
	at app//org.testng.TestRunner.run(TestRunner.java:602)
	at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at app//org.testng.TestNG.runSuites(TestNG.java:1099)
	at app//org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

testCreateDirectory

org.apache.hadoop.ipc.RemoteException(java.lang.NoClassDefFoundError): Could not initialize class org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol.getDescriptor(ClientNamenodeProtocolProtos.java)
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.getDescriptorForType(ClientNamenodeProtocolProtos.java)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573)
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227)
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246)
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712)
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439)
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953)
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203)

	at app//org.apache.hadoop.ipc.Client.getRpcResponse(Client.java:1584)
	at app//org.apache.hadoop.ipc.Client.call(Client.java:1529)
	at app//org.apache.hadoop.ipc.Client.call(Client.java:1426)
	at app//org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:258)
	at app//org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:139)
	at app/jdk.proxy3/jdk.proxy3.$Proxy60.getDatanodeReport(Unknown Source)
	at app//org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.lambda$getDatanodeReport$28(ClientNamenodeProtocolTranslatorPB.java:713)
	at app//org.apache.hadoop.ipc.internal.ShadedProtobufHelper.ipc(ShadedProtobufHelper.java:160)
	at app//org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.getDatanodeReport(ClientNamenodeProtocolTranslatorPB.java:713)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:437)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeMethod(RetryInvocationHandler.java:170)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invoke(RetryInvocationHandler.java:162)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeOnce(RetryInvocationHandler.java:100)
	at app//org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:366)
	at app/jdk.proxy3/jdk.proxy3.$Proxy61.getDatanodeReport(Unknown Source)
	at app//org.apache.hadoop.hdfs.DFSClient.datanodeReport(DFSClient.java:2134)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2869)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2920)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.startDataNodes(MiniDFSCluster.java:1848)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.initMiniDFSCluster(MiniDFSCluster.java:995)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster.<init>(MiniDFSCluster.java:594)
	at app//org.apache.hadoop.hdfs.MiniDFSCluster$Builder.build(MiniDFSCluster.java:533)
	at app//org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:30)
	at app//org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:38)
	at app//org.broadinstitute.hellbender.utils.io.IOUtilsUnitTest.testCreateDirectory(IOUtilsUnitTest.java:543)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568)
	at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511)
	at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
	at app//org.testng.TestRunner.run(TestRunner.java:602)
	at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at app//org.testng.TestNG.runSuites(TestNG.java:1099)
	at app//org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

Tests

Test	Duration	Result
testAppendPathToDir	0.415s	failed
testCreateDirectory	1.155s	failed
testCreateFifoFile	0.012s	passed
testCreateFifoFileThrows	0.004s	passed
testCreateTempFileInDirectory	0.001s	passed
testCreateTempFileWithContent	0.001s	passed
testDeleteDirOnExit	0s	passed
testDeleteRecursively	0.001s	passed
testExtractTarGzOverwrite	0.071s	passed
testExtractTarGzThrowsExceptionOnExistingOutput	0.035s	passed
testExtractTarGz[0](null)	0.054s	passed
testExtractTarGz[1](/tmp/provideForTestExtractTarGz_Case210111061273022256702)	0.035s	passed
testGenomicsDBPathParsing[0](null, null, null, false)	0.001s	passed
testGenomicsDBPathParsing[10](gendb., null, null, false)	0s	passed
testGenomicsDBPathParsing[11](gendb.dfdfdf://fdfdf, dfdfdf://fdfdf, gendb.dfdfdf://fdfdf, true)	0.001s	passed
testGenomicsDBPathParsing[12](gendb://fdfdf, fdfdf, gendb:///home/runner/work/gatk/gatk/fdfdf, true)	0s	passed
testGenomicsDBPathParsing[13](gendb:///fdfd, /fdfd, gendb:///fdfd, true)	0s	passed
testGenomicsDBPathParsing[14](gendb:///, /, gendb:///, true)	0s	passed
testGenomicsDBPathParsing[15](gendb.hdfs://this-node:9000/dir, hdfs://this-node:9000/dir, gendb.hdfs://this-node:9000/dir, true)	0s	passed
testGenomicsDBPathParsing[16](gendb.gs://my-bucket/dir, gs://my-bucket/dir, gendb.gs://my-bucket/dir, true)	0s	passed
testGenomicsDBPathParsing[17](gendb.s3://my-bucket/dir, s3://my-bucket/dir, gendb.s3://my-bucket/dir, true)	0s	passed
testGenomicsDBPathParsing[18](gendb-hdfs://this-node:9000/dir, null, null, false)	0s	passed
testGenomicsDBPathParsing[19](gendb-gs://this-node:9000/dir, null, null, false)	0s	passed
testGenomicsDBPathParsing[1](, null, null, false)	0s	passed
testGenomicsDBPathParsing[2](dfdfdf://fdfdf, null, null, false)	0s	passed
testGenomicsDBPathParsing[3](fdfdf, null, null, false)	0s	passed
testGenomicsDBPathParsing[4](gendbdfdfdf://fdfdf, null, null, false)	0s	passed
testGenomicsDBPathParsing[5](gendb-dfdfdf://fdfdf, null, null, false)	0s	passed
testGenomicsDBPathParsing[6](gendb, null, null, false)	0s	passed
testGenomicsDBPathParsing[7](gendbdfdf, null, null, false)	0s	passed
testGenomicsDBPathParsing[8](agendb://dfdfd, null, null, false)	0s	passed
testGenomicsDBPathParsing[9](gendb.://fdfdf, null, null, false)	0s	passed
testGetAbsolutePathWithoutFileProtocol[0](relative/example.txt, /home/runner/work/gatk/gatk/relative/example.txt)	0s	passed
testGetAbsolutePathWithoutFileProtocol[1](/local/example.txt, /local/example.txt)	0s	passed
testGetAbsolutePathWithoutFileProtocol[2](/local/file://example.txt, /local/file:/example.txt)	0s	passed
testGetAbsolutePathWithoutFileProtocol[3](file:///local/example.txt, /local/example.txt)	0s	passed
testGetAbsolutePathWithoutFileProtocol[4](gs://dir/example.txt, gs://dir/example.txt)	0.010s	passed
testGetPathHandlesIntervals	0.005s	passed
testIsHDF5File[0](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isValidHDF5.hdf5, true)	0.001s	passed
testIsHDF5File[1](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils/isValidHDF5.ext, true)	0.001s	passed
testIsHDF5File[2](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isTSV.tsv, false)	0s	passed
testIsHDF5File[3](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isTSV.hdf, false)	0.001s	passed
testIsHDF5File[4](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isTSV.hdf5, false)	0s	passed
testIsHDF5File[5](src/test/resources/org/broadinstitute/hellbender/utils/io/IOUtils//isEmpty.txt, false)	0s	passed
testIsSpecialFile	0s	passed
testReadNonExistentFileIntoByteArray	0.001s	passed
testReadStreamIntoByteArrayInvalidBufferSize	0s	passed
testRemoveExtension[0]()	0.001s	passed
testRemoveExtension[1](/path/to)	0s	passed
testRemoveExtension[2](gs://bucket/subdir)	0s	passed
testReplaceExtension[0](file.old, file.new)	0s	passed
testReplaceExtension[1](file.something.old, file.something.new)	0s	passed
testReplaceExtension[2](src/test.something/file, src/test.something/file.new)	0s	passed
testReplaceExtension[3](/.src.folder/some/thing/.secret/file.old, /.src.folder/some/thing/.secret/file.new)	0s	passed
testSuccessfulCanReadFileCheck	0s	passed
testSuccessfulCanReadFilesCheck	0s	passed
testTempDir	0.001s	passed
testTempPath[0](/tmp/local14338818500996187746)	0.001s	passed
testTempPath[1](tmp)	0.005s	passed
testUnsuccessfulCanReadFileCheck[0](/tmp/Utils-can-read-file-Dir9120295879168503514)	0s	passed
testUnsuccessfulCanReadFileCheck[1](/tmp/Utils-cant-read-NoFile1115243852491499023.file)	0s	passed
testUnsuccessfulCanReadFileCheck[2](/tmp/Utils-cant-read-NotReadable10224002256449359576.file)	0s	passed
testUrlEncodeDecode[0](string, string)	0s	passed
testUrlEncodeDecode[1](string., string.)	0s	passed
testUrlEncodeDecode[2](string1, string1)	0s	passed
testUrlEncodeDecode[3](string with space, string+with+space)	0s	passed
testUrlEncodeDecode[4](string://, string%3A%2F%2F)	0s	passed
testWriteTarGz	0.269s	passed
testWriteTempResourceFromPath[0](large/testResourceFile.txt, null, this is a test resource file)	0.001s	passed
testWriteTempResourceFromPath[1](testResourceFile.txt, class org.broadinstitute.hellbender.utils.io.IOUtils, this is a test resource file)	0.001s	passed
testWriteTempResource[0](large/testResourceFile.txt, null, this is a test resource file)	0.003s	passed
testWriteTempResource[1](testResourceFile.txt, class org.broadinstitute.hellbender.utils.io.IOUtils, this is a test resource file)	0.001s	passed
testWriteThenReadFileIntoByteArray[0](0, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[10](10000, 4096)	0.001s	passed
testWriteThenReadFileIntoByteArray[1](1, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[2](2000, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[3](4095, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[4](4096, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[5](4097, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[6](6000, 4096)	0.001s	passed
testWriteThenReadFileIntoByteArray[7](8191, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[8](8192, 4096)	0s	passed
testWriteThenReadFileIntoByteArray[9](8193, 4096)	0s	passed
testWriteThenReadStreamIntoByteArray[0](0, 4096)	0s	passed
testWriteThenReadStreamIntoByteArray[10](10000, 4096)	0s	passed
testWriteThenReadStreamIntoByteArray[1](1, 4096)	0s	passed
testWriteThenReadStreamIntoByteArray[2](2000, 4096)	0.001s	passed
testWriteThenReadStreamIntoByteArray[3](4095, 4096)	0s	passed
testWriteThenReadStreamIntoByteArray[4](4096, 4096)	0s	passed
testWriteThenReadStreamIntoByteArray[5](4097, 4096)	0s	passed
testWriteThenReadStreamIntoByteArray[6](6000, 4096)	0.001s	passed
testWriteThenReadStreamIntoByteArray[7](8191, 4096)	0s	passed
testWriteThenReadStreamIntoByteArray[8](8192, 4096)	0s	passed
testWriteThenReadStreamIntoByteArray[9](8193, 4096)	0s	passed

Standard error

22:41:44.312 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
22:41:44.334 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
22:41:44.341 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
22:41:44.524 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
22:41:44.628 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
22:41:44.646 WARN  Server - IPC Server handler 0 on default port 46141, call Call#3 Retry#0 org.apache.hadoop.hdfs.server.protocol.DatanodeProtocol.versionRequest from localhost:46506 / 127.0.0.1:46506
java.lang.NoClassDefFoundError: Could not initialize class org.apache.hadoop.hdfs.protocol.proto.DatanodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.DatanodeProtocolProtos$DatanodeProtocolService.getDescriptor(DatanodeProtocolProtos.java:34977) ~[hadoop-hdfs-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.protocol.proto.DatanodeProtocolProtos$DatanodeProtocolService$2.getDescriptorForType(DatanodeProtocolProtos.java:34750) ~[hadoop-hdfs-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169) ~[hadoop-common-3.4.0.jar:?]
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712) [?:?]
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439) [?:?]
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953) [hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203) [hadoop-common-3.4.0.jar:?]
22:41:44.647 WARN  DataNode - Problem connecting to server: localhost/127.0.0.1:46141
22:41:44.648 WARN  Server - IPC Server handler 1 on default port 46141, call Call#4 Retry#0 org.apache.hadoop.hdfs.protocol.ClientProtocol.getDatanodeReport from localhost:46514 / 127.0.0.1:46514
java.lang.NoClassDefFoundError: Could not initialize class org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol.getDescriptor(ClientNamenodeProtocolProtos.java) ~[hadoop-hdfs-client-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.getDescriptorForType(ClientNamenodeProtocolProtos.java) ~[hadoop-hdfs-client-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169) ~[hadoop-common-3.4.0.jar:?]
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712) [?:?]
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439) [?:?]
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953) [hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203) [hadoop-common-3.4.0.jar:?]
22:41:44.649 WARN  Server - IPC Server handler 2 on default port 46141, call Call#5 Retry#0 org.apache.hadoop.hdfs.protocol.ClientProtocol.getDatanodeReport from localhost:46514 / 127.0.0.1:46514
java.lang.NoClassDefFoundError: Could not initialize class org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol.getDescriptor(ClientNamenodeProtocolProtos.java) ~[hadoop-hdfs-client-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.getDescriptorForType(ClientNamenodeProtocolProtos.java) ~[hadoop-hdfs-client-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169) ~[hadoop-common-3.4.0.jar:?]
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712) [?:?]
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439) [?:?]
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953) [hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203) [hadoop-common-3.4.0.jar:?]
22:41:44.650 WARN  MiniDFSCluster - Tried waitActive() 2 time(s) and failed, giving up.  org.apache.hadoop.ipc.RemoteException(java.lang.NoClassDefFoundError): Could not initialize class org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol.getDescriptor(ClientNamenodeProtocolProtos.java)
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.getDescriptorForType(ClientNamenodeProtocolProtos.java)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573)
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227)
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246)
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712)
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439)
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953)
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203)

	at org.apache.hadoop.ipc.Client.getRpcResponse(Client.java:1584)
	at org.apache.hadoop.ipc.Client.call(Client.java:1529)
	at org.apache.hadoop.ipc.Client.call(Client.java:1426)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:258)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:139)
	at jdk.proxy3/jdk.proxy3.$Proxy60.getDatanodeReport(Unknown Source)
	at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.lambda$getDatanodeReport$28(ClientNamenodeProtocolTranslatorPB.java:713)
	at org.apache.hadoop.ipc.internal.ShadedProtobufHelper.ipc(ShadedProtobufHelper.java:160)
	at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.getDatanodeReport(ClientNamenodeProtocolTranslatorPB.java:713)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:437)
	at org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeMethod(RetryInvocationHandler.java:170)
	at org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invoke(RetryInvocationHandler.java:162)
	at org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeOnce(RetryInvocationHandler.java:100)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:366)
	at jdk.proxy3/jdk.proxy3.$Proxy61.getDatanodeReport(Unknown Source)
	at org.apache.hadoop.hdfs.DFSClient.datanodeReport(DFSClient.java:2134)
	at org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2869)
	at org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2920)
	at org.apache.hadoop.hdfs.MiniDFSCluster.startDataNodes(MiniDFSCluster.java:1848)
	at org.apache.hadoop.hdfs.MiniDFSCluster.initMiniDFSCluster(MiniDFSCluster.java:995)
	at org.apache.hadoop.hdfs.MiniDFSCluster.<init>(MiniDFSCluster.java:594)
	at org.apache.hadoop.hdfs.MiniDFSCluster$Builder.build(MiniDFSCluster.java:533)
	at org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:30)
	at org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:38)
	at org.broadinstitute.hellbender.utils.io.IOUtilsUnitTest.testAppendPathToDir(IOUtilsUnitTest.java:476)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

22:41:44.655 ERROR DataNode - Command processor encountered interrupt and exit.
22:41:44.655 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
22:41:44.655 ERROR DataNode - Initialization failed for Block pool <registering> (Datanode Uuid unassigned) service to localhost/127.0.0.1:46141. Exiting. 
java.io.IOException: DN shut down before block pool connected
	at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.retrieveNamespaceInfo(BPServiceActor.java:276) ~[hadoop-hdfs-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.connectToNNAndHandshake(BPServiceActor.java:306) ~[hadoop-hdfs-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.run(BPServiceActor.java:889) [hadoop-hdfs-3.4.0.jar:?]
	at java.base/java.lang.Thread.run(Thread.java:833) [?:?]
22:41:44.655 WARN  DataNode - Ending block pool service for: Block pool <registering> (Datanode Uuid unassigned) service to localhost/127.0.0.1:46141
22:41:44.656 WARN  DataSetLockManager - not open lock leak check func
22:41:44.728 WARN  MetricsConfig - Cannot locate configuration: tried hadoop-metrics2-namenode.properties,hadoop-metrics2.properties
22:41:44.747 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
22:41:44.753 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
22:41:45.669 WARN  AuthenticationFilter - Unable to initialize FileSignerSecretProvider, falling back to use random secrets. Reason: Could not read signature secret file: /home/runner/hadoop-http-auth-signature-secret
22:41:45.770 WARN  DatanodeHttpServer - Got null for restCsrfPreventionFilter - will not do any filtering.
22:41:45.798 WARN  Server - IPC Server handler 0 on default port 40795, call Call#6 Retry#0 org.apache.hadoop.hdfs.server.protocol.DatanodeProtocol.versionRequest from localhost:43472 / 127.0.0.1:43472
java.lang.NoClassDefFoundError: Could not initialize class org.apache.hadoop.hdfs.protocol.proto.DatanodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.DatanodeProtocolProtos$DatanodeProtocolService.getDescriptor(DatanodeProtocolProtos.java:34977) ~[hadoop-hdfs-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.protocol.proto.DatanodeProtocolProtos$DatanodeProtocolService$2.getDescriptorForType(DatanodeProtocolProtos.java:34750) ~[hadoop-hdfs-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169) ~[hadoop-common-3.4.0.jar:?]
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712) [?:?]
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439) [?:?]
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953) [hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203) [hadoop-common-3.4.0.jar:?]
22:41:45.799 WARN  DataNode - Problem connecting to server: localhost/127.0.0.1:40795
22:41:45.802 WARN  Server - IPC Server handler 1 on default port 40795, call Call#7 Retry#0 org.apache.hadoop.hdfs.protocol.ClientProtocol.getDatanodeReport from localhost:43482 / 127.0.0.1:43482
java.lang.NoClassDefFoundError: Could not initialize class org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol.getDescriptor(ClientNamenodeProtocolProtos.java) ~[hadoop-hdfs-client-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.getDescriptorForType(ClientNamenodeProtocolProtos.java) ~[hadoop-hdfs-client-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169) ~[hadoop-common-3.4.0.jar:?]
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712) [?:?]
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439) [?:?]
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953) [hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203) [hadoop-common-3.4.0.jar:?]
22:41:45.803 WARN  Server - IPC Server handler 2 on default port 40795, call Call#8 Retry#0 org.apache.hadoop.hdfs.protocol.ClientProtocol.getDatanodeReport from localhost:43482 / 127.0.0.1:43482
java.lang.NoClassDefFoundError: Could not initialize class org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol.getDescriptor(ClientNamenodeProtocolProtos.java) ~[hadoop-hdfs-client-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.getDescriptorForType(ClientNamenodeProtocolProtos.java) ~[hadoop-hdfs-client-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246) ~[hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169) ~[hadoop-common-3.4.0.jar:?]
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712) [?:?]
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439) [?:?]
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953) [hadoop-common-3.4.0.jar:?]
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203) [hadoop-common-3.4.0.jar:?]
22:41:45.804 WARN  MiniDFSCluster - Tried waitActive() 2 time(s) and failed, giving up.  org.apache.hadoop.ipc.RemoteException(java.lang.NoClassDefFoundError): Could not initialize class org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol.getDescriptor(ClientNamenodeProtocolProtos.java)
	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.getDescriptorForType(ClientNamenodeProtocolProtos.java)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:604)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:589)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine2.java:573)
	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1227)
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1246)
	at org.apache.hadoop.ipc.Server$RpcCall.run(Server.java:1169)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:712)
	at java.base/javax.security.auth.Subject.doAs(Subject.java:439)
	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1953)
	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:3203)

	at org.apache.hadoop.ipc.Client.getRpcResponse(Client.java:1584)
	at org.apache.hadoop.ipc.Client.call(Client.java:1529)
	at org.apache.hadoop.ipc.Client.call(Client.java:1426)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:258)
	at org.apache.hadoop.ipc.ProtobufRpcEngine2$Invoker.invoke(ProtobufRpcEngine2.java:139)
	at jdk.proxy3/jdk.proxy3.$Proxy60.getDatanodeReport(Unknown Source)
	at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.lambda$getDatanodeReport$28(ClientNamenodeProtocolTranslatorPB.java:713)
	at org.apache.hadoop.ipc.internal.ShadedProtobufHelper.ipc(ShadedProtobufHelper.java:160)
	at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.getDatanodeReport(ClientNamenodeProtocolTranslatorPB.java:713)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:437)
	at org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeMethod(RetryInvocationHandler.java:170)
	at org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invoke(RetryInvocationHandler.java:162)
	at org.apache.hadoop.io.retry.RetryInvocationHandler$Call.invokeOnce(RetryInvocationHandler.java:100)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:366)
	at jdk.proxy3/jdk.proxy3.$Proxy61.getDatanodeReport(Unknown Source)
	at org.apache.hadoop.hdfs.DFSClient.datanodeReport(DFSClient.java:2134)
	at org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2869)
	at org.apache.hadoop.hdfs.MiniDFSCluster.waitActive(MiniDFSCluster.java:2920)
	at org.apache.hadoop.hdfs.MiniDFSCluster.startDataNodes(MiniDFSCluster.java:1848)
	at org.apache.hadoop.hdfs.MiniDFSCluster.initMiniDFSCluster(MiniDFSCluster.java:995)
	at org.apache.hadoop.hdfs.MiniDFSCluster.<init>(MiniDFSCluster.java:594)
	at org.apache.hadoop.hdfs.MiniDFSCluster$Builder.build(MiniDFSCluster.java:533)
	at org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:30)
	at org.broadinstitute.hellbender.testutils.MiniClusterUtils.getMiniCluster(MiniClusterUtils.java:38)
	at org.broadinstitute.hellbender.utils.io.IOUtilsUnitTest.testCreateDirectory(IOUtilsUnitTest.java:543)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
	at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

22:41:45.811 ERROR DataNode - Command processor encountered interrupt and exit.
22:41:45.811 WARN  DataNode - Ending command processor service for: Thread[Command processor,5,main]
22:41:45.811 ERROR DataNode - Initialization failed for Block pool <registering> (Datanode Uuid unassigned) service to localhost/127.0.0.1:40795. Exiting. 
java.io.IOException: DN shut down before block pool connected
	at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.retrieveNamespaceInfo(BPServiceActor.java:276) ~[hadoop-hdfs-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.connectToNNAndHandshake(BPServiceActor.java:306) ~[hadoop-hdfs-3.4.0.jar:?]
	at org.apache.hadoop.hdfs.server.datanode.BPServiceActor.run(BPServiceActor.java:889) [hadoop-hdfs-3.4.0.jar:?]
	at java.base/java.lang.Thread.run(Thread.java:833) [?:?]
22:41:45.811 WARN  DataNode - Ending block pool service for: Block pool <registering> (Datanode Uuid unassigned) service to localhost/127.0.0.1:40795
22:41:45.811 WARN  DataSetLockManager - not open lock leak check func
22:41:45.830 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testCreateFifoFile8486537233396693463/FIFOFILE
22:41:45.970 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/
22:41:45.971 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc1/
22:41:45.971 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc2/
22:41:45.971 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc3/
22:41:45.972 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/MANIFEST.txt
22:41:45.972 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/README.txt
22:41:45.973 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc3/hg19/
22:41:45.973 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc3/hg38/
22:41:45.973 WARN  IOUtils - File already exists in path.  Replacing existing file: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc3/hg38/
22:41:45.973 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc3/hg19/familial.config
22:41:45.974 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc3/hg19/Familial_Cancer_Genes.no_dupes.tsv
22:41:45.974 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc2/hg19/
22:41:45.975 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc2/hg38/
22:41:45.975 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc2/hg38/gencode_xrefseq.config
22:41:45.975 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc2/hg38/gencode_xrefseq_v90_38.tsv
22:41:45.991 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc2/hg19/gencode_xrefseq.config
22:41:45.992 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc2/hg19/gencode_xrefseq_v75_37.tsv
22:41:46.001 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc1/hg19/
22:41:46.002 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc1/hg38/
22:41:46.002 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc1/hg38/cancer_gene_census.config
22:41:46.002 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc1/hg38/CancerGeneCensus_Table_1_full_2012-03-15.txt
22:41:46.003 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.20180524T145835.csv
22:41:46.003 WARN  IOUtils - Overwriting existing output destination: file:///tmp/IOUtilsUnitTest_testExtractTarGz7162662554132759252/dummyDataSources/dummySrc1/hg19/dnaRepairGenes.config