java.lang.RuntimeException: java.util.zip.DataFormatException: invalid distance too far back

sourceforge.net | 4 months ago
  1. 0

    SAM tools / Mailing Lists

    sourceforge.net | 4 months ago
    java.lang.RuntimeException: java.util.zip.DataFormatException: invalid distance too far back
  2. 0

    “java.lang.NegativeArraySizeException” when I run gatk_AddorReplaceReadgroups - GATK-Forum

    broadinstitute.org | 1 year ago
    java.lang.RuntimeException: BGZF file has invalid uncompressedLength: -667232877
  3. 0

    “java.lang.NegativeArraySizeException” when I run picard_AddorReplaceReadgroups [Archive] - SEQanswers

    seqanswers.com | 1 month ago
    java.lang.RuntimeException: BGZF file has invalid uncompressedLength: -667232877
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  5. 0

    Control flow is too big

    YouTrack | 3 years ago
    java.lang.RuntimeException: Control flow is too big. It will be great if you sent the file back to us to analyse.
  6. 0

    I use the following configuration {code} <integration:channel id="myChannel"> <integration:queue capacity="10" /> </integration:channel> <integration:transformer id="myTransformer" ref="myBean" method="myMethod" input-channel="myChannel" output-channel="someOutputChannel"> </integration:transformer> <integration:service-activator input-channel="errorChannel" output-channel="someOtherOutputChannel" ref="myBean" method="handleError"> </integration:service-activator> <alias name="defaultBean" alias="myBean" /> <bean id="defaultBean" class="org.beans.impl.DefaultBean" /> {code} * myBean.myMethod does throw a RuntimeException. * when i start the first process everything works as expected. myMethod is called, exception is catched and I receive a message in the errorChannel * when i start the second process, the exception is not catched by the errorChannel. It shows the following log instead: {code} ERROR [task-scheduler-10] [ErrorHandler] unexpected exception caught org.springframework.integration.MessageHandlingException: java.lang.RuntimeException: too bad at org.springframework.integration.handler.MethodInvokingMessageProcessor.processMessage(MethodInvokingMessageProcessor.java:76) at org.springframework.integration.handler.ServiceActivatingHandler.handleRequestMessage(ServiceActivatingHandler.java:64) at org.springframework.integration.handler.AbstractReplyProducingMessageHandler.handleMessageInternal(AbstractReplyProducingMessageHandler.java:97) at org.springframework.integration.handler.AbstractMessageHandler.handleMessage(AbstractMessageHandler.java:73) at org.springframework.integration.endpoint.PollingConsumer.doPoll(PollingConsumer.java:70) at org.springframework.integration.endpoint.AbstractPollingEndpoint$1.call(AbstractPollingEndpoint.java:146) at org.springframework.integration.endpoint.AbstractPollingEndpoint$1.call(AbstractPollingEndpoint.java:144) at org.springframework.integration.endpoint.AbstractPollingEndpoint$Poller$1.run(AbstractPollingEndpoint.java:207) at org.springframework.integration.util.ErrorHandlingTaskExecutor$1.run(ErrorHandlingTaskExecutor.java:52) at org.springframework.core.task.SyncTaskExecutor.execute(SyncTaskExecutor.java:48) at org.springframework.integration.util.ErrorHandlingTaskExecutor.execute(ErrorHandlingTaskExecutor.java:49) at org.springframework.integration.endpoint.AbstractPollingEndpoint$Poller.run(AbstractPollingEndpoint.java:202) at org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:53) at org.springframework.scheduling.concurrent.ReschedulingRunnable.run(ReschedulingRunnable.java:81) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:206) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:680) Caused by: java.lang.RuntimeException: too bad at org.wonderlandcore.services.impl.DefaultFileImportService.parseFile(DefaultFileImportService.java:92) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:318) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at org.springframework.aop.aspectj.MethodInvocationProceedingJoinPoint.proceed(MethodInvocationProceedingJoinPoint.java:80) at org.wonderlandcore.aop.MasterTenantAspect.setTenant(MasterTenantAspect.java:24) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethodWithGivenArgs(AbstractAspectJAdvice.java:621) at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethod(AbstractAspectJAdvice.java:610) at org.springframework.aop.aspectj.AspectJAroundAdvice.invoke(AspectJAroundAdvice.java:65) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy25.parseFile(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.expression.spel.support.ReflectiveMethodExecutor.execute(ReflectiveMethodExecutor.java:69) at org.springframework.expression.spel.ast.MethodReference.getValueInternal(MethodReference.java:84) at org.springframework.expression.spel.ast.CompoundExpression.getValueInternal(CompoundExpression.java:57) at org.springframework.expression.spel.ast.SpelNodeImpl.getTypedValue(SpelNodeImpl.java:102) at org.springframework.expression.spel.standard.SpelExpression.getValue(SpelExpression.java:102) at org.springframework.integration.util.AbstractExpressionEvaluator.evaluateExpression(AbstractExpressionEvaluator.java:126) at org.springframework.integration.util.MessagingMethodInvokerHelper.processInternal(MessagingMethodInvokerHelper.java:225) at org.springframework.integration.util.MessagingMethodInvokerHelper.process(MessagingMethodInvokerHelper.java:125) at org.springframework.integration.handler.MethodInvokingMessageProcessor.processMessage(MethodInvokingMessageProcessor.java:73) ... 21 more {code}

    Spring JIRA | 4 years ago | Bastian Echterhoelter
    org.springframework.integration.MessageHandlingException: java.lang.RuntimeException: too bad

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    Root Cause Analysis

    1. java.lang.RuntimeException

      java.util.zip.DataFormatException: invalid distance too far back

      at net.sf.samtools.util.BlockGunzipper.unzipBlock()
    2. picard
      BlockCompressedInputStream.read
      1. net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:112)
      2. net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:320)
      3. net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:302)
      4. net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:106)
      5. net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:175)
      5 frames
    3. Java RT
      DataInputStream.read
      1. java.io.DataInputStream.read(DataInputStream.java:149)
      1 frame
    4. picard
      AddOrReplaceReadGroups.main
      1. net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394)
      2. net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371)
      3. net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480)
      4. net.sf.samtools.util.BinaryCodec.readInt(BinaryCodec.java:491)
      5. net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:159)
      6. net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:486)
      7. net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:460)
      8. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:450)
      9. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:417)
      10. net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:629)
      11. net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:607)
      12. net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:91)
      13. net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:169)
      14. net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
      15. net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61)
      15 frames