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/local15243704403060221796/printReadsRefBundle1210509235774612854.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle2292152064650698561.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle12729860660575808134.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle10483948185643998143.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle13406773240918953132.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle6082211822898961334.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle3645610798832913054.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle17258478511434668058.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle16080122310281236089.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle9982265306313378480.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle15558271804151500499.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle13108678048569862278.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle15392417030842165114.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle2209295671792417496.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle16982341205075264118.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle4822619754550741353.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileUsingReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle17091716213840438611.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle17784489243927700624.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle10482576488045976748.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle17162332994539437570.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle5142659205237524776.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle6458649880638855212.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle9780820657596492045.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle16862457658501994074.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle9406030087194311046.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle16586364816945037463.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle18137434577503775555.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle2703876961579345324.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle8888857260814650862.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@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle912593583513728078.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle178960057129127166.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle16243704809761748894.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle12700930541053988396.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
testFileToFileWithReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta)
org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile: Couldn't read the given reference, reference must be a .fasta or .2bit file. Reference provided was: /tmp/local15243704403060221796/printReadsRefBundle9444716209527647517.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@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at app//org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) at java.base@17.0.6/java.util.ArrayList.forEach(ArrayList.java:1511) at app//org.testng.TestRunner.privateRun(TestRunner.java:829) at app//org.testng.TestRunner.run(TestRunner.java:602) at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437) at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) at app//org.testng.SuiteRunner.run(SuiteRunner.java:330) at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176) at app//org.testng.TestNG.runSuites(TestNG.java:1099) at app//org.testng.TestNG.run(TestNG.java:1067) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base@17.0.6/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base@17.0.6/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base@17.0.6/java.lang.reflect.Method.invoke(Method.java:568) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92) at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source) at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200) at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103) at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63) at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121) at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Tests
| Test | Duration | Result |
|---|---|---|
| testCoordinateSortedInRegion | 2.489s | 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) | 0.078s | 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) | 0.073s | failed |
| testFileToFileUsingReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.082s | failed |
| testFileToFileUsingReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.102s | failed |
| testFileToFileUsingReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.086s | 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) | 0.075s | failed |
| testFileToFileUsingReferenceBundle[21](print_reads.sorted.queryname.bam, .sam, null) | 0.001s | passed |
| testFileToFileUsingReferenceBundle[22](print_reads.sorted.queryname.bam, .bam, null) | 0s | passed |
| testFileToFileUsingReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.079s | failed |
| testFileToFileUsingReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.079s | failed |
| testFileToFileUsingReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.077s | failed |
| testFileToFileUsingReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.074s | failed |
| testFileToFileUsingReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.081s | failed |
| testFileToFileUsingReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.076s | failed |
| testFileToFileUsingReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta) | 0.081s | 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) | 0.090s | failed |
| testFileToFileUsingReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta) | 0.076s | failed |
| testFileToFileUsingReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta) | 0.092s | failed |
| testFileToFileUsingReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta) | 0.077s | failed |
| testFileToFileUsingReferenceBundle[9](print_reads.sorted.sam, .sam, null) | 0s | passed |
| testFileToFileWithReferenceBundle[0](print_reads.sam, .sam, null) | 0.199s | passed |
| testFileToFileWithReferenceBundle[10](print_reads.sorted.sam, .bam, null) | 0.208s | passed |
| testFileToFileWithReferenceBundle[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.075s | failed |
| testFileToFileWithReferenceBundle[12](print_reads.sorted.bam, .sam, null) | 0.252s | passed |
| testFileToFileWithReferenceBundle[13](print_reads.sorted.bam, .bam, null) | 0.269s | passed |
| testFileToFileWithReferenceBundle[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.074s | failed |
| testFileToFileWithReferenceBundle[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.074s | failed |
| testFileToFileWithReferenceBundle[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.073s | failed |
| testFileToFileWithReferenceBundle[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.069s | failed |
| testFileToFileWithReferenceBundle[18](print_reads.sorted.queryname.sam, .sam, null) | 0.206s | passed |
| testFileToFileWithReferenceBundle[19](print_reads.sorted.queryname.sam, .bam, null) | 0.194s | passed |
| testFileToFileWithReferenceBundle[1](print_reads.sam, .bam, null) | 0.205s | passed |
| testFileToFileWithReferenceBundle[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.073s | failed |
| testFileToFileWithReferenceBundle[21](print_reads.sorted.queryname.bam, .sam, null) | 0.356s | passed |
| testFileToFileWithReferenceBundle[22](print_reads.sorted.queryname.bam, .bam, null) | 0.381s | passed |
| testFileToFileWithReferenceBundle[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.072s | failed |
| testFileToFileWithReferenceBundle[24](print_reads.sorted.queryname.cram, .sam, print_reads.fasta) | 0.072s | failed |
| testFileToFileWithReferenceBundle[25](print_reads.sorted.queryname.cram, .bam, print_reads.fasta) | 0.077s | failed |
| testFileToFileWithReferenceBundle[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.074s | failed |
| testFileToFileWithReferenceBundle[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.073s | failed |
| testFileToFileWithReferenceBundle[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.073s | failed |
| testFileToFileWithReferenceBundle[2](print_reads.sam, .cram, print_reads.fasta) | 0.074s | failed |
| testFileToFileWithReferenceBundle[3](print_reads.bam, .sam, null) | 0.359s | passed |
| testFileToFileWithReferenceBundle[4](print_reads.bam, .bam, null) | 0.357s | passed |
| testFileToFileWithReferenceBundle[5](print_reads.bam, .cram, print_reads.fasta) | 0.071s | failed |
| testFileToFileWithReferenceBundle[6](print_reads.cram, .sam, print_reads.fasta) | 0.067s | failed |
| testFileToFileWithReferenceBundle[7](print_reads.cram, .bam, print_reads.fasta) | 0.074s | failed |
| testFileToFileWithReferenceBundle[8](print_reads.cram, .cram, print_reads.fasta) | 0.071s | failed |
| testFileToFileWithReferenceBundle[9](print_reads.sorted.sam, .sam, null) | 0.171s | passed |
| testFileToFile[0](print_reads.sam, .sam, null) | 0.363s | passed |
| testFileToFile[10](print_reads.sorted.sam, .bam, null) | 0.224s | passed |
| testFileToFile[11](print_reads.sorted.sam, .cram, print_reads.fasta) | 0.204s | passed |
| testFileToFile[12](print_reads.sorted.bam, .sam, null) | 0.280s | passed |
| testFileToFile[13](print_reads.sorted.bam, .bam, null) | 0.315s | passed |
| testFileToFile[14](print_reads.sorted.bam, .cram, print_reads.fasta) | 0.284s | passed |
| testFileToFile[15](print_reads.sorted.cram, .sam, print_reads.fasta) | 0.258s | passed |
| testFileToFile[16](print_reads.sorted.cram, .bam, print_reads.fasta) | 0.269s | passed |
| testFileToFile[17](print_reads.sorted.cram, .cram, print_reads.fasta) | 0.245s | passed |
| testFileToFile[18](print_reads.sorted.queryname.sam, .sam, null) | 0.190s | passed |
| testFileToFile[19](print_reads.sorted.queryname.sam, .bam, null) | 0.214s | passed |
| testFileToFile[1](print_reads.sam, .bam, null) | 0.344s | passed |
| testFileToFile[20](print_reads.sorted.queryname.sam, .cram, print_reads.fasta) | 0.206s | passed |
| testFileToFile[21](print_reads.sorted.queryname.bam, .sam, null) | 0.353s | passed |
| testFileToFile[22](print_reads.sorted.queryname.bam, .bam, null) | 0.382s | passed |
| testFileToFile[23](print_reads.sorted.queryname.bam, .cram, print_reads.fasta) | 0.375s | 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) | 0.317s | passed |
| testFileToFile[26](print_reads.sorted.queryname.cram, .cram, print_reads.fasta) | 0.325s | passed |
| testFileToFile[27](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .cram, print_reads.fasta) | 0.315s | passed |
| testFileToFile[28](print_reads.sorted.queryname.htsjdk-2.1.0.cram, .sam, print_reads.fasta) | 0.318s | passed |
| testFileToFile[2](print_reads.sam, .cram, print_reads.fasta) | 0.357s | passed |
| testFileToFile[3](print_reads.bam, .sam, null) | 0.445s | passed |
| testFileToFile[4](print_reads.bam, .bam, null) | 0.448s | passed |
| testFileToFile[5](print_reads.bam, .cram, print_reads.fasta) | 0.447s | passed |
| testFileToFile[6](print_reads.cram, .sam, print_reads.fasta) | 0.409s | passed |
| testFileToFile[7](print_reads.cram, .bam, print_reads.fasta) | 0.353s | passed |
| testFileToFile[8](print_reads.cram, .cram, print_reads.fasta) | 0.374s | passed |
| testFileToFile[9](print_reads.sorted.sam, .sam, null) | 0.216s | passed |
| testNonExistentReference | 0.077s | passed |
| testReadAndWriteCRAMAndReferenceOnHDFS | 5.179s | passed |
| testReadFiltering | 0.194s | passed |
| testReadFiltering_asIntegrationTestSpec | 0.194s | passed |
| testReadFilters[0](print_reads_one_malformed_read.sam, null, .sam, [], 7) | 0.170s | passed |
| testReadFilters[10](print_reads.sorted.bam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 101], 8) | 0.244s | 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) | 0.251s | 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) | 0.218s | passed |
| testReadFilters[1](print_reads_one_malformed_read.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.190s | passed |
| testReadFilters[2](print_reads_one_malformed_read.sam, null, .sam, [--disable-read-filter, WellformedReadFilter], 8) | 0.176s | passed |
| testReadFilters[3](print_reads.sorted.sam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.163s | passed |
| testReadFilters[4](print_reads.sorted.sam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.175s | passed |
| testReadFilters[5](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 100, --max-read-length, 200], 8) | 0.186s | passed |
| testReadFilters[6](print_reads.sorted.sam, null, .sam, [--read-filter, ReadLengthReadFilter, --min-read-length, 1, --max-read-length, 10], 0) | 0.161s | 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) | 0.168s | passed |
| testReadFilters[8](print_reads.sorted.bam, null, .sam, [--disable-tool-default-read-filters], 8) | 0.243s | passed |
| testReadFilters[9](print_reads.sorted.bam, null, .sam, [--read-filter, ReadNameReadFilter, --read-name, both_reads_align_clip_adapter], 2) | 0.246s | passed |
| testReadThatConsumesNoReferenceBases | 0.274s | passed |
| testSBIIndexGranularityArgument[0](1) | 0.428s | passed |
| testSBIIndexGranularityArgument[1](100) | 0.357s | passed |
| testSequenceDictionaryValidation | 0.094s | passed |
| testUnSorted | 0.255s | passed |
| testUnSortedRoundTrip | 0.193s | passed |
| testUnmappedReadInclusion[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [unmapped], [u1, u2, u3, u4, u5]) | 0.273s | passed |
| testUnmappedReadInclusion[10](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000009-10000011, unmapped], [a, b, c, d, e, g, h, h, i, i]) | 0.596s | passed |
| testUnmappedReadInclusion[11](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /home/runner/work/gatk/gatk/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]) | 0.530s | passed |
| testUnmappedReadInclusion[1](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped.intervals], [u1, u2, u3, u4, u5]) | 0.265s | passed |
| testUnmappedReadInclusion[2](/home/runner/work/gatk/gatk/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]) | 0.269s | passed |
| testUnmappedReadInclusion[3](/home/runner/work/gatk/gatk/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]) | 0.259s | passed |
| testUnmappedReadInclusion[4](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_with_unmapped.bam, null, [/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped2.intervals], [a, b, c, k, u1, u2, u3, u4, u5]) | 0.272s | passed |
| testUnmappedReadInclusion[5](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam, null, [unmapped], [g, h, h, i, i]) | 0.261s | passed |
| testUnmappedReadInclusion[6](/home/runner/work/gatk/gatk/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]) | 0.261s | passed |
| testUnmappedReadInclusion[7](/home/runner/work/gatk/gatk/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]) | 0.271s | passed |
| testUnmappedReadInclusion[8](/home/runner/work/gatk/gatk/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]) | 0.280s | passed |
| testUnmappedReadInclusion[9](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [unmapped], [g, h, h, i, i]) | 0.353s | passed |
Standard output
-------------------------------------------------------------------------------- [13:48:26] Executing test PrintReadsSparkIntegrationTest:testReadFiltering_asIntegrationTestSpec
Standard error
[May 27, 2025 at 1:48:11 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:11 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:11 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:12 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:12 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:13 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:13 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:14 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:14 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:14 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:15 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:15 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:15 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:15 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:16 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:17 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:17 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:17 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:17 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:18 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:18 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:18 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:19 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:19 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:19 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:20 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:21 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:22 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:22 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:22 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:22 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:23 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:24 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:25 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:25 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:25 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:25 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:25 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:26 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:27 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:28 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:28 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:28 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:28 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:29 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:29 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:29 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:29 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:29 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:30 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:30 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:30 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:31 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:31 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:31 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:31 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:32 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:32 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:32 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=524288000 [May 27, 2025 at 1:48:33 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=589299712 [May 27, 2025 at 1:48:33 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=895483904 [May 27, 2025 at 1:48:38 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=895483904 13:48:38.997 ERROR DataNode - Command processor encountered interrupt and exit. [May 27, 2025 at 1:48:39 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=895483904 [May 27, 2025 at 1:48:39 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=895483904 [May 27, 2025 at 1:48:39 PM UTC] org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=895483904