Exception parsing clustal file java.io.IOException: Stream closed
java.io.IOException: Stream closed
at java.base/java.io.BufferedReader.ensureOpen(BufferedReader.java:122)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:319)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:392)
at jalview.io.FileParse.nextLine(FileParse.java:590)
at jalview.io.ClustalFile.parse(ClustalFile.java:74)
at jalview.io.ClustalFileTest.__CLR4_4_1copn7j44lz(ClustalFileTest.java:79)
at jalview.io.ClustalFileTest.testParse_noNumbering(ClustalFileTest.java:64)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1541)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
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:94)
at com.sun.proxy.$Proxy2.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:133)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Exception parsing clustal file java.io.IOException: Stream closed
java.io.IOException: Stream closed
at java.base/java.io.BufferedReader.ensureOpen(BufferedReader.java:122)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:319)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:392)
at jalview.io.FileParse.nextLine(FileParse.java:590)
at jalview.io.ClustalFile.parse(ClustalFile.java:74)
at jalview.io.ClustalFileTest.__CLR4_4_15qbi1044lp(ClustalFileTest.java:53)
at jalview.io.ClustalFileTest.testParse_withNumbering(ClustalFileTest.java:36)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1541)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
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$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
at com.sun.proxy.$Proxy2.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:133)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)