java.lang.IllegalStateException: Could not read the fastaFileInputStream.

GitHub | yoyohashao | 4 months ago
  1. 0

    ERROR:Is there something wrong with my JVM?

    GitHub | 4 months ago | yoyohashao
    java.lang.IllegalStateException: Could not read the fastaFileInputStream.
  2. 0

    Resolving "IOException: Underlying input stream returned zero bytes" errors

    Oracle Community | 10 years ago | 843790
    java.io.IOException: Underlying input stream returned zero bytes
  3. 0

    An unknown error occurred while attempting to perform this command

    GitHub | 2 years ago | tech-boy101
    java.io.IOException: The handle is invalid
  4. Speed up your debug routine!

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  5. 0

    /help menu bug?

    GitHub | 2 years ago | gofirst2220
    java.io.IOException: The handle is invalid

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Root Cause Analysis

  1. java.io.IOException

    Is a directory

    at sun.nio.ch.FileDispatcherImpl.read0()
  2. Java RT
    BufferedReader.readLine
    1. sun.nio.ch.FileDispatcherImpl.read0(Native Method)
    2. sun.nio.ch.FileDispatcherImpl.read(FileDispatcherImpl.java:46)
    3. sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)
    4. sun.nio.ch.IOUtil.read(IOUtil.java:197)
    5. sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:159)
    6. sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
    7. sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
    8. sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
    9. sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
    10. sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
    11. sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
    12. java.io.InputStreamReader.read(InputStreamReader.java:184)
    13. java.io.BufferedReader.fill(BufferedReader.java:161)
    14. java.io.BufferedReader.readLine(BufferedReader.java:324)
    15. java.io.BufferedReader.readLine(BufferedReader.java:389)
    15 frames
  3. uk.ac.ebi
    LoadFastaFileImpl.loadSequences
    1. uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:62)
    1 frame
  4. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    4. java.lang.reflect.Method.invoke(Method.java:498)
    4 frames
  5. Spring AOP
    ReflectiveMethodInvocation.proceed
    1. org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
    2. org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    3. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    3 frames
  6. Spring Tx
    TransactionInterceptor.invoke
    1. org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
    2. org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
    3. org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    3 frames
  7. Spring AOP
    JdkDynamicAopProxy.invoke
    1. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    2. org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
    2 frames
  8. com.sun.proxy
    $Proxy93.loadSequences
    1. com.sun.proxy.$Proxy93.loadSequences(Unknown Source)
    1 frame
  9. uk.ac.ebi
    StepExecutionTransactionImpl.executeInTransaction
    1. uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:245)
    2. uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
    2 frames
  10. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    4. java.lang.reflect.Method.invoke(Method.java:498)
    4 frames
  11. Spring AOP
    ReflectiveMethodInvocation.proceed
    1. org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
    2. org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    3. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    3 frames
  12. Spring Tx
    TransactionInterceptor.invoke
    1. org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
    2. org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
    3. org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    3 frames
  13. Spring AOP
    JdkDynamicAopProxy.invoke
    1. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    2. org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
    2 frames
  14. com.sun.proxy
    $Proxy96.executeInTransaction
    1. com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source)
    1 frame
  15. uk.ac.ebi
    LocalJobQueueListener.onMessage
    1. uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189)
    1 frame
  16. Spring Framework
    DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run
    1. org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
    2. org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
    3. org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
    4. org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
    5. org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
    6. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
    7. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
    8. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
    8 frames
  17. Java RT
    Thread.run
    1. java.lang.Thread.run(Thread.java:745)
    1 frame