Class org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest
|
72%
successful |
Failed tests
testFileToFileUsingReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle8537364014585999626.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle1199180016852987817.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle16734801670400697850.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle13069690674644670876.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle2166211167318814237.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle2613309278446732627.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle3254319320337512368.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle3255811837709330382.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle9365730785236882900.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle4465519018329288568.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle7439936210023556821.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle11309425208942900716.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle646282245722597763.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle9906248859722576301.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle4511011009053423570.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle9690892172195630057.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle6947957438780896792.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:158) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle7250604455955884241.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle14579377652752206480.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle9264973317892077377.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle13501634235655782518.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle11571004478136528164.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle1760153997868770158.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle7420344635444898972.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle8449321437203182889.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle13309349171968163610.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle6197009213123622303.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle12805405020182219439.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle17782372426693137484.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle2635584187835151373.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle15314924385137376129.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle7203933682949540847.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle1314831876376866582.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local13774000465916765003/printReadsRefBundle16381061853807595525.json at app//org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.<init>(ReferenceMultiSparkSource.java:52) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:592) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:542) at app//org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:533) at app//org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31) 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.tools.AbstractPrintReadsIntegrationTest.doFileToFile(AbstractPrintReadsIntegrationTest.java:68) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.doFileToFileUsingReferenceBundle(AbstractPrintReadsIntegrationTest.java:94) at app//org.broadinstitute.hellbender.tools.AbstractPrintReadsIntegrationTest.testFileToFileWithReferenceBundle(AbstractPrintReadsIntegrationTest.java:110) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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@17.0.12/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@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569) 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 |
|---|---|---|
| testCoordinateSortedInRegion | 2.409s | passed |
| testFileToFileUsingReferenceBundle[0](print_reads.sam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[10](print_reads.sorted.sam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.110s | failed |
| testFileToFileUsingReferenceBundle[12](print_reads.sorted.bam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[13](print_reads.sorted.bam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.103s | failed |
| testFileToFileUsingReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.128s | failed |
| testFileToFileUsingReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.103s | failed |
| testFileToFileUsingReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.095s | failed |
| testFileToFileUsingReferenceBundle[18](print_reads.sorted.queryname.sam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[19](print_reads.sorted.queryname.sam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[1](print_reads.sam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.095s | failed |
| testFileToFileUsingReferenceBundle[21](print_reads.sorted.queryname.bam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[22](print_reads.sorted.queryname.bam, .bam, null) | 0.001s | passed |
| testFileToFileUsingReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.091s | failed |
| testFileToFileUsingReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.098s | failed |
| testFileToFileUsingReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.092s | failed |
| testFileToFileUsingReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.106s | failed |
| testFileToFileUsingReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.100s | failed |
| testFileToFileUsingReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.090s | failed |
| testFileToFileUsingReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta) | 0.103s | failed |
| testFileToFileUsingReferenceBundle[3](print_reads.bam, .sam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[4](print_reads.bam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta) | 0.106s | failed |
| testFileToFileUsingReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta) | 0.129s | failed |
| testFileToFileUsingReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta) | 0.104s | failed |
| testFileToFileUsingReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta) | 0.104s | failed |
| testFileToFileUsingReferenceBundle[9](print_reads.sorted.sam, .sam, null) | 0s | passed |
| testFileToFileWithReferenceBundle[0](print_reads.sam, .sam, null) | 0.194s | passed |
| testFileToFileWithReferenceBundle[10](print_reads.sorted.sam, .bam, null) | 0.195s | passed |
| testFileToFileWithReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.097s | failed |
| testFileToFileWithReferenceBundle[12](print_reads.sorted.bam, .sam, null) | 0.260s | passed |
| testFileToFileWithReferenceBundle[13](print_reads.sorted.bam, .bam, null) | 0.282s | passed |
| testFileToFileWithReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.099s | failed |
| testFileToFileWithReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.103s | failed |
| testFileToFileWithReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.097s | failed |
| testFileToFileWithReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.093s | failed |
| testFileToFileWithReferenceBundle[18](print_reads.sorted.queryname.sam, .sam, null) | 0.206s | passed |
| testFileToFileWithReferenceBundle[19](print_reads.sorted.queryname.sam, .bam, null) | 0.193s | passed |
| testFileToFileWithReferenceBundle[1](print_reads.sam, .bam, null) | 0.202s | passed |
| testFileToFileWithReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.090s | failed |
| testFileToFileWithReferenceBundle[21](print_reads.sorted.queryname.bam, .sam, null) | 0.350s | passed |
| testFileToFileWithReferenceBundle[22](print_reads.sorted.queryname.bam, .bam, null) | 0.361s | passed |
| testFileToFileWithReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.095s | failed |
| testFileToFileWithReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.103s | failed |
| testFileToFileWithReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.101s | failed |
| testFileToFileWithReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.095s | failed |
| testFileToFileWithReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.094s | failed |
| testFileToFileWithReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.096s | failed |
| testFileToFileWithReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta) | 0.099s | failed |
| testFileToFileWithReferenceBundle[3](print_reads.bam, .sam, null) | 0.374s | passed |
| testFileToFileWithReferenceBundle[4](print_reads.bam, .bam, null) | 0.364s | passed |
| testFileToFileWithReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta) | 0.101s | failed |
| testFileToFileWithReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta) | 0.104s | failed |
| testFileToFileWithReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta) | 0.098s | failed |
| testFileToFileWithReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta) | 0.095s | failed |
| testFileToFileWithReferenceBundle[9](print_reads.sorted.sam, .sam, null) | 0.181s | passed |
| testFileToFile[0](print_reads.sam, .sam, null) | 0.383s | passed |
| testFileToFile[10](print_reads.sorted.sam, .bam, null) | 0.229s | passed |
| testFileToFile[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.216s | passed |
| testFileToFile[12](print_reads.sorted.bam, .sam, null) | 0.283s | passed |
| testFileToFile[13](print_reads.sorted.bam, .bam, null) | 0.295s | passed |
| testFileToFile[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.298s | passed |
| testFileToFile[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.249s | passed |
| testFileToFile[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.260s | passed |
| testFileToFile[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.265s | passed |
| testFileToFile[18](print_reads.sorted.queryname.sam, .sam, null) | 0.203s | passed |
| testFileToFile[19](print_reads.sorted.queryname.sam, .bam, null) | 0.208s | passed |
| testFileToFile[1](print_reads.sam, .bam, null) | 0.307s | passed |
| testFileToFile[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.219s | passed |
| testFileToFile[21](print_reads.sorted.queryname.bam, .sam, null) | 0.358s | passed |
| testFileToFile[22](print_reads.sorted.queryname.bam, .bam, null) | 0.415s | passed |
| testFileToFile[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.376s | passed |
| testFileToFile[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.333s | passed |
| testFileToFile[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.331s | passed |
| testFileToFile[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.345s | passed |
| testFileToFile[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.325s | passed |
| testFileToFile[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.308s | passed |
| testFileToFile[2](print_reads.sam, .cram, print_reads.fasta) | 0.346s | passed |
| testFileToFile[3](print_reads.bam, .sam, null) | 0.535s | passed |
| testFileToFile[4](print_reads.bam, .bam, null) | 0.503s | passed |
| testFileToFile[5](print_reads.bam, .cram, print_reads.fasta) | 0.463s | passed |
| testFileToFile[6](print_reads.cram, .sam, print_reads.fasta) | 0.380s | passed |
| testFileToFile[7](print_reads.cram, .bam, print_reads.fasta) | 0.408s | passed |
| testFileToFile[8](print_reads.cram, .cram, print_reads.fasta) | 0.364s | passed |
| testFileToFile[9](print_reads.sorted.sam, .sam, null) | 0.220s | passed |
| testNonExistentReference | 0.101s | passed |
| testReadAndWriteCRAMAndReferenceOnHDFS | - | ignored |
| testReadFiltering | 0.188s | passed |
| testReadFiltering_asIntegrationTestSpec | 0.190s | passed |
| testReadFilters[0](print_reads_one_malformed_read.sam, null, .sam, [], 7) | 0.180s | passed |
| testReadFilters[10](print_reads.sorted.bam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 8) | 0.269s | passed |
| testReadFilters[11](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter, --read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 2) | 0.259s | passed |
| testReadFilters[12](print_reads.sorted.cram, print_reads.fasta, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter, --read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 2) | 0.246s | passed |
| testReadFilters[1](print_reads_one_malformed_read.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.168s | passed |
| testReadFilters[2](print_reads_one_malformed_read.sam, null, .sam, [--disable-read-filter, WellformedReadFilter], 8) | 0.174s | passed |
| testReadFilters[3](print_reads.sorted.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.171s | passed |
| testReadFilters[4](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.178s | passed |
| testReadFilters[5](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 200], 8) | 0.175s | passed |
| testReadFilters[6](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 1, --max-read-length, 10], 0) | 0.174s | passed |
| testReadFilters[7](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter, --read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 2) | 0.172s | passed |
| testReadFilters[8](print_reads.sorted.bam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.250s | passed |
| testReadFilters[9](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.269s | passed |
| testReadThatConsumesNoReferenceBases | 0.279s | passed |
| testSBIIndexGranularityArgument[0](1) | 0.365s | passed |
| testSBIIndexGranularityArgument[1](100) | 0.350s | passed |
| testSequenceDictionaryValidation | 0.122s | passed |
| testUnSorted | 0.260s | passed |
| testUnSortedRoundTrip | 0.193s | passed |
| testUnmappedReadInclusion[0](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [unmapped], [u1, u2, u3, u4, u5]) | 0.285s | passed |
| testUnmappedReadInclusion[10](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000011, unmapped], [a, b, c, d, e, g, h, h, i, i]) | 0.443s | passed |
| testUnmappedReadInclusion[11](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000013, unmapped], [a, b, c, d, e, f, f, g, h, h, i, i]) | 0.430s | passed |
| testUnmappedReadInclusion[1](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped.intervals], [u1, u2, u3, u4, u5]) | 0.280s | passed |
| testUnmappedReadInclusion[2](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [1:200-300, unmapped], [a, b, c, u1, u2, u3, u4, u5]) | 0.268s | passed |
| testUnmappedReadInclusion[3](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [1:200-300, 4:700-701, unmapped], [a, b, c, k, u1, u2, u3, u4, u5]) | 0.274s | passed |
| testUnmappedReadInclusion[4](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped2.intervals], [a, b, c, k, u1, u2, u3, u4, u5]) | 0.267s | passed |
| testUnmappedReadInclusion[5](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [unmapped], [g, h, h, i, i]) | 0.272s | passed |
| testUnmappedReadInclusion[6](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [20:10000009-10000011], [a, b, c, d, e]) | 0.266s | passed |
| testUnmappedReadInclusion[7](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [20:10000009-10000011, unmapped], [a, b, c, d, e, g, h, h, i, i]) | 0.284s | passed |
| testUnmappedReadInclusion[8](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [20:10000009-10000013, unmapped], [a, b, c, d, e, f, f, g, h, h, i, i]) | 0.271s | passed |
| testUnmappedReadInclusion[9](/gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /gatkCloneMountPoint/src/test/resources/large/human_g1k_v37.20.21.fasta, [unmapped], [g, h, h, i, i]) | 0.388s | passed |
Standard output
-------------------------------------------------------------------------------- [16:00:35] Executing test PrintReadsSparkIntegrationTest:testReadFiltering_asIntegrationTestSpec
Standard error
[May 19, 2025 at 4:00:19 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:19 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:19 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:20 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:20 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:21 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:21 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:22 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:22 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:22 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:23 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:23 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:23 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:23 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 19, 2025 at 4:00:24 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:24 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:24 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:24 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:25 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:25 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:25 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:25 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:26 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:26 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:26 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:27 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:27 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:27 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:28 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:28 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:28 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:28 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:28 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:28 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:29 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:30 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:30 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:30 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:30 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:30 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:30 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:30 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:31 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:32 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:32 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:32 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:32 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:32 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:33 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:34 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:35 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:36 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:36 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:36 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:36 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:36 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:37 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:37 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:37 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:37 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:38 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:38 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:38 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:38 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:38 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:39 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:39 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:39 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:40 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:41 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=629145600 [May 19, 2025 at 4:00:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=694157312 [May 19, 2025 at 4:00:42 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=694157312 [May 19, 2025 at 4:00:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=960495616 [May 19, 2025 at 4:00:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=960495616 [May 19, 2025 at 4:00:43 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=960495616