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java.lang.IllegalStateException: Command line failed with exit code: 1 #103

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zhangycbnu opened this issue Sep 9, 2019 · 2 comments
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java.lang.IllegalStateException: Command line failed with exit code: 1 #103

zhangycbnu opened this issue Sep 9, 2019 · 2 comments

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@zhangycbnu
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Hi there,

I have an issue when I run InterProScan-5.31-70.0 with TMHMM application. Not sure how to fix it. Could you please give me some suggestion?

Here is the log info:

09/09/2019 09:42:38:808 Welcome to InterProScan-5.31-70.0
09/09/2019 09:42:45:058 Running InterProScan v5 in STANDALONE mode... on Linux
09/09/2019 09:42:55:822 Loading file /path/user/example/test.fasta
09/09/2019 09:42:55:828 Running the following analyses:
[TMHMM-2.0c]
Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete...
09/09/2019 09:42:59:978 28% completed
2019-09-09 09:43:05,151 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 1
Command: bin/tmhmm/2.0c/decodeanhmm data/tmhmm/2.0c/TMHMM2.0c.model /path/user/example/temp/myserver_20190909_094245047_hh2u//jobTMHMM/000000000001_000000010001.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 0.061 0.040 0.068 0.022 0.057 0.056 0.093 0.025 0.045 0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032
Error output from binary:
decodeanhmm 1.1g
Copyright (C) 1998 by Anders Krogh
Mon Sep 9 10:43:05 2019

Error: Couldn't open file asta

2019-09-09 09:43:05,157 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:204] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: bin/tmhmm/2.0c/decodeanhmm data/tmhmm/2.0c/TMHMM2.0c.model /path/user/example/temp/mysever_20190909_094245047_hh2u//jobTMHMM/000000000001_000000010001.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 0.061 0.040 0.068 0.022 0.057 0.056 0.093 0.025 0.045 0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032
Error output from binary:
decodeanhmm 1.1g
Copyright (C) 1998 by Anders Krogh
Mon Sep 9 10:43:05 2019

Error: Couldn't open file asta

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy107.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:192)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)

2019-09-09 09:43:05,158 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:206] ERROR - StepExecution with errors - stepName: stepTMHMMRunBinary
2019-09-09 09:43:05,225 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:143] WARN - StepInstance 4 is being re-run following a failure.
2019-09-09 09:43:10,344 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 1
Command: bin/tmhmm/2.0c/decodeanhmm data/tmhmm/2.0c/TMHMM2.0c.model //path/user/example/emp/myserver_20190909_094245047_hh2u//jobTMHMM/000000000001_000000010001.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 0.061 0.040 0.068 0.022 0.057 0.056 0.093 0.025 0.045 0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032
Error output from binary:
decodeanhmm 1.1g
Copyright (C) 1998 by Anders Krogh
Mon Sep 9 10:43:10 2019

Error: Couldn't open file asta

2019-09-09 09:43:10,345 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:204] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: bin/tmhmm/2.0c/decodeanhmm data/tmhmm/2.0c/TMHMM2.0c.model /path/user/example/temp/myserver_20190909_094245047_hh2u//jobTMHMM/000000000001_000000010001.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 0.061 0.040 0.068 0.022 0.057 0.056 0.093 0.025 0.045 0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032
Error output from binary:
decodeanhmm 1.1g
Copyright (C) 1998 by Anders Krogh
Mon Sep 9 10:43:10 2019

Error: Couldn't open file asta

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy107.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:192)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)

2019-09-09 09:43:10,346 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:206] ERROR - StepExecution with errors - stepName: stepTMHMMRunBinary
2019-09-09 09:43:10,432 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:143] WARN - StepInstance 4 is being re-run following a failure.
2019-09-09 09:43:15,553 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:188] ERROR - Command line failed with exit code: 1
Command: bin/tmhmm/2.0c/decodeanhmm data/tmhmm/2.0c/TMHMM2.0c.model //path/user/example/temp/myserver_20190909_094245047_hh2u//jobTMHMM/000000000001_000000010001.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 0.061 0.040 0.068 0.022 0.057 0.056 0.093 0.025 0.045 0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032
Error output from binary:
decodeanhmm 1.1g
Copyright (C) 1998 by Anders Krogh
Mon Sep 9 10:43:15 2019

Error: Couldn't open file asta

2019-09-09 09:43:15,554 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:204] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: bin/tmhmm/2.0c/decodeanhmm data/tmhmm/2.0c/TMHMM2.0c.model /path/user/example//temp/myserver_20190909_094245047_hh2u//jobTMHMM/000000000001_000000010001.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 0.061 0.040 0.068 0.022 0.057 0.056 0.093 0.025 0.045 0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032
Error output from binary:
decodeanhmm 1.1g
Copyright (C) 1998 by Anders Krogh
Mon Sep 9 10:43:15 2019

Error: Couldn't open file asta

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:190)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy107.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:192)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039)
at java.lang.Thread.run(Thread.java:745)

2019-09-09 09:43:15,555 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:206] ERROR - StepExecution with errors - stepName: stepTMHMMRunBinary
2019-09-09 09:43:15,579 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 4 : Run TMHMM binary for selected protein sequences for proteins 1 to 10001 has failed irretrievably. Available StackTraces follow.
2019-09-09 09:43:15,580 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2019-09-09 09:43:15,580 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:258] ERROR - Exception thrown by StandaloneBlackBoxMaster:
java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information.
at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:42)
at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:134)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:377)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

Best,
Yancong
@gsn7
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gsn7 commented Sep 10, 2019

there is a bug in TMHMM where if the fasta file path has more than 230 characters it throws the error you are getting. you can either

  1. use a directory path that is not very long so the final path is still less than 230 characters or
  2. use Phobius as Phobius will give you almost all predictions that you get when using TMHMM

@zhangycbnu
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Great! Now the issue has been fixed. Thanks a lot!

@gsn7 gsn7 closed this as completed Sep 25, 2019
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@zhangycbnu @gsn7