Class org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest

all > org.broadinstitute.hellbender.tools.reference > CompareReferencesIntegrationTest
23

tests
6

failures
0

ignored
1.442s

duration
73%

successful

Failed tests

testFullAlignmentMode[0](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2multiplesnps.fasta, hg19mini.fasta_hg19mini_chr2multiplesnps.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr2multiplesnps.fasta.vcf)

org.broadinstitute.hellbender.exceptions.UserException: Unable to run MUMmer aligner: GATK does not contain a MUMmer distribution for system architecture aarch64 on operating system Linux
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.selectCorrectMummerDistributionForPlatform(MummerExecutor.java:64)
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.<init>(MummerExecutor.java:50)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.runFullAlignment(CompareReferences.java:293)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.traverse(CompareReferences.java:192)
	at app//org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest.testFullAlignmentMode(CompareReferencesIntegrationTest.java:290)
	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)

testFullAlignmentMode[1](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, hg19mini.fasta_hg19mini_chr1indel.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testDeletion.hg19mini.fasta_hg19mini_chr1indel.fasta.vcf)

org.broadinstitute.hellbender.exceptions.UserException: Unable to run MUMmer aligner: GATK does not contain a MUMmer distribution for system architecture aarch64 on operating system Linux
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.selectCorrectMummerDistributionForPlatform(MummerExecutor.java:64)
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.<init>(MummerExecutor.java:50)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.runFullAlignment(CompareReferences.java:293)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.traverse(CompareReferences.java:192)
	at app//org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest.testFullAlignmentMode(CompareReferencesIntegrationTest.java:290)
	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)

testFullAlignmentMode[2](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, hg19mini_chr1indel.fasta_hg19mini.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testInsertion.hg19mini_chr1indel.fasta_hg19mini.fasta.vcf)

org.broadinstitute.hellbender.exceptions.UserException: Unable to run MUMmer aligner: GATK does not contain a MUMmer distribution for system architecture aarch64 on operating system Linux
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.selectCorrectMummerDistributionForPlatform(MummerExecutor.java:64)
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.<init>(MummerExecutor.java:50)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.runFullAlignment(CompareReferences.java:293)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.traverse(CompareReferences.java:192)
	at app//org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest.testFullAlignmentMode(CompareReferencesIntegrationTest.java:290)
	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)

testFullAlignmentMode[3](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_snpsmultiplecontigs.fasta, hg19mini.fasta_hg19mini_snpsmultiplecontigs.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_snpsmultiplecontigs.fasta.vcf)

org.broadinstitute.hellbender.exceptions.UserException: Unable to run MUMmer aligner: GATK does not contain a MUMmer distribution for system architecture aarch64 on operating system Linux
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.selectCorrectMummerDistributionForPlatform(MummerExecutor.java:64)
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.<init>(MummerExecutor.java:50)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.runFullAlignment(CompareReferences.java:293)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.traverse(CompareReferences.java:192)
	at app//org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest.testFullAlignmentMode(CompareReferencesIntegrationTest.java:290)
	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)

testFullAlignmentMode[4](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_snpandindel.fasta, hg19mini.fasta_hg19mini_snpandindel.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.SNPandINDEL.hg19mini.fasta_hg19mini_snpandindel.fasta.vcf)

org.broadinstitute.hellbender.exceptions.UserException: Unable to run MUMmer aligner: GATK does not contain a MUMmer distribution for system architecture aarch64 on operating system Linux
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.selectCorrectMummerDistributionForPlatform(MummerExecutor.java:64)
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.<init>(MummerExecutor.java:50)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.runFullAlignment(CompareReferences.java:293)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.traverse(CompareReferences.java:192)
	at app//org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest.testFullAlignmentMode(CompareReferencesIntegrationTest.java:290)
	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)

testFullAlignmentMode[5](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_manySNPsINDELs.fasta, hg19mini.fasta_hg19mini_manySNPsINDELs.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_manySNPsINDELs.fasta.vcf)

org.broadinstitute.hellbender.exceptions.UserException: Unable to run MUMmer aligner: GATK does not contain a MUMmer distribution for system architecture aarch64 on operating system Linux
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.selectCorrectMummerDistributionForPlatform(MummerExecutor.java:64)
	at app//org.broadinstitute.hellbender.utils.alignment.MummerExecutor.<init>(MummerExecutor.java:50)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.runFullAlignment(CompareReferences.java:293)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferences.traverse(CompareReferences.java:192)
	at app//org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
	at app//org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
	at app//org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
	at app//org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
	at app//org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
	at app//org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:108)
	at app//org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest.testFullAlignmentMode(CompareReferencesIntegrationTest.java:290)
	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
testCompareReferencesMD5CalculationModes[0](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2snp.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testCompareReferencesMissingValue.table, USE_DICT) 0.061s passed
testCompareReferencesMD5CalculationModes[1](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_missingmd5.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2snp.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testCompareReferencesRecalculateIfMissing.table, RECALCULATE_IF_MISSING) 0.065s passed
testCompareReferencesMD5CalculationModes[2](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_missingmd5.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2snp.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testCompareReferencesAlwaysRecalculateMD5.table, ALWAYS_RECALCULATE) 0.070s passed
testCompareReferencesMissingValue 0.061s passed
testCompareReferencesMultipleReferences 0.062s passed
testCompareReferencesRenamedSequence 0.061s passed
testCompareReferencesToStdOutput 0.060s passed
testCompareReferencesUseDictMD5MissingValue 0.060s passed
testFindSNPsMoreThanTwoReferences[0](FULL_ALIGNMENT) 0.060s passed
testFindSNPsMoreThanTwoReferences[1](FIND_SNPS_ONLY) 0.059s passed
testFindSNPsNoOutputDir[0](FULL_ALIGNMENT) 0.060s passed
testFindSNPsNoOutputDir[1](FIND_SNPS_ONLY) 0.061s passed
testFindSNPsNonexistentOutputDir[0](FULL_ALIGNMENT) 0.061s passed
testFindSNPsNonexistentOutputDir[1](FIND_SNPS_ONLY) 0.060s passed
testFindSNPs[0](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2multiplesnps.fasta, hg19mini.fasta_hg19mini_chr2multiplesnps.fasta_snps.tsv, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr2multiplesnps.fasta_snps.tsv) 0.068s passed
testFindSNPs[1](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2iupacsnps.fasta, hg19mini.fasta_hg19mini_chr2iupacsnps.fasta_snps.tsv, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr2iupacsnps.fasta_snps.tsv) 0.065s passed
testFindSNPs[2](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, hg19mini.fasta_hg19mini_chr1indel.fasta_snps.tsv, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr1indel.fasta_snps.tsv) 0.062s passed
testFullAlignmentMode[0](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2multiplesnps.fasta, hg19mini.fasta_hg19mini_chr2multiplesnps.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr2multiplesnps.fasta.vcf) 0.065s failed
testFullAlignmentMode[1](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, hg19mini.fasta_hg19mini_chr1indel.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testDeletion.hg19mini.fasta_hg19mini_chr1indel.fasta.vcf) 0.064s failed
testFullAlignmentMode[2](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, hg19mini_chr1indel.fasta_hg19mini.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testInsertion.hg19mini_chr1indel.fasta_hg19mini.fasta.vcf) 0.063s failed
testFullAlignmentMode[3](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_snpsmultiplecontigs.fasta, hg19mini.fasta_hg19mini_snpsmultiplecontigs.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_snpsmultiplecontigs.fasta.vcf) 0.065s failed
testFullAlignmentMode[4](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_snpandindel.fasta, hg19mini.fasta_hg19mini_snpandindel.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.SNPandINDEL.hg19mini.fasta_hg19mini_snpandindel.fasta.vcf) 0.065s failed
testFullAlignmentMode[5](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_manySNPsINDELs.fasta, hg19mini.fasta_hg19mini_manySNPsINDELs.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_manySNPsINDELs.fasta.vcf) 0.064s failed

Standard output

*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini_missingmd5.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini_missingmd5.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_1renamed.fasta
Status:
	DIFFER_IN_SEQUENCE_NAMES

REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

REFERENCE PAIR: hg19mini_1renamed.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE_NAMES
	DIFFER_IN_SEQUENCE

*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_1renamed.fasta
Status:
	DIFFER_IN_SEQUENCE_NAMES

MD5	Length	hg19mini.fasta	hg19mini_chr2snp.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	1
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
600ccbfe836f04b26c0eea36dd0485ee	16000	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2snp.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr2multiplesnps.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	1
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
a1cdf5289fd7c56ec9be9e2d47695a76	16000	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2multiplesnps.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr2iupacsnps.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
eee82532c1dea7dc57397d4205648f13	16000	---	1
a1cdf5289fd7c56ec9be9e2d47695a76	16000	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2iupacsnps.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr1indel.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	2
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
dfbdb1a2666f8be18b140f07fd80df3a	15920	---	1
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr1indel.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr2multiplesnps.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	1
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
a1cdf5289fd7c56ec9be9e2d47695a76	16000	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr2multiplesnps.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_chr1indel.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	2
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
dfbdb1a2666f8be18b140f07fd80df3a	15920	---	1
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_chr1indel.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini_chr1indel.fasta	hg19mini.fasta
dfbdb1a2666f8be18b140f07fd80df3a	15920	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	2
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
8c0c38e352d8f3309eabe4845456f274	16000	---	1
*********************************************************
REFERENCE PAIR: hg19mini_chr1indel.fasta, hg19mini.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_snpsmultiplecontigs.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	---
a16d5419e3aa3b4756b0d4d19f2e6e8f	16000	---	1
cf05678991b4b337be1e39d3c9db6154	16000	---	2
02a72810239374ce9cb60fc664b43eef	16000	---	4
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_snpsmultiplecontigs.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_snpandindel.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	---
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	---
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	4
483d5c08a04f1ba7beb1d49b25898ced	16000	---	1
a7a6b3d28b24b2457ffd6e4f4762b8a5	15920	---	2
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_snpandindel.fasta
Status:
	DIFFER_IN_SEQUENCE

MD5	Length	hg19mini.fasta	hg19mini_manySNPsINDELs.fasta
8c0c38e352d8f3309eabe4845456f274	16000	1	1
5f8388fe3fb34aa38375ae6cf5e45b89	16000	2	2
94de808a3a2203dbb02434a47bd8184f	16000	3	3
7d397ee919e379328d8f52c57a54c778	16000	4	---
5f5f6e0928c1216cc68a6ca80ce3c38b	16080	---	4
*********************************************************
REFERENCE PAIR: hg19mini.fasta, hg19mini_manySNPsINDELs.fasta
Status:
	DIFFER_IN_SEQUENCE

Standard error

[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:58 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784
[October 27, 2025 at 5:44:59 PM UTC] org.broadinstitute.hellbender.tools.reference.CompareReferences done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=3128950784