Problem running interproscan-5.15-54.0 for protein sequences

Question

[yangyongzhi2008]

Hello,

I am using the standalone interproscan-5.15-54.0. I could run the given test_proteins file sucessfully however, when I am trying to run my protein sequences, it gives same errors. This is the sam question in biostar (Problem running interproscan-5.14-53.0 for protein sequences), but I can't find any useful information. Please help me.

The following is the running information:

$ /home/share/software/interproscan/interproscan-5.15-54.0/interproscan.sh -i test.fa -o test.fa.tsv -f tsv
08/11/2015 02:24:55:869 Welcome to InterProScan-5.15-54.0
08/11/2015 02:25:11:769 Running InterProScan v5 in STANDALONE mode...
Loading file /home/pool/users/yangyongzhi2012/Ostrya_genome/annotation/function/InterproScan-test/test.fa
08/11/2015 02:25:27:450 Running the following analyses:
[jobProDom-2006.1,jobHAMAP,jobPanther,jobSMART-6.2,jobSuperFamily-1.75,jobPRINTS-42.0,jobPIRSF-3.01,jobPfam,jobGene3d,jobCoils,jobPrositeProfiles,jobTIGRFAM-15.0,jobPrositePatterns]
Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally.
08/11/2015 02:25:49:471 26% completed
2015-11-08 02:26:02,744 [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:192] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
java.lang.ArrayIndexOutOfBoundsException: 10
        at uk.ac.ebi.interpro.scan.io.match.prints.PrintsMatchParser.parse(PrintsMatchParser.java:78)
        at uk.ac.ebi.interpro.scan.management.model.implementations.prints.ParsePrintsOutputStep.execute(ParsePrintsOutputStep.java:74)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
        at sun.reflect.GeneratedMethodAccessor66.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
        at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:180)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessag$ListenerContainer.java:326)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1071)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1063)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:960)
        at java.lang.Thread.run(Thread.java:724)2015-11-08 02:26:02,855 [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:58] WARN - StepInstance 40 is being re-run following a failure.
08/11/2015 02:26:09:463 52% completed
08/11/2015 02:26:16:760 75% completed
2015-11-08 02:26:18,035 [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:192] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
java.lang.ArrayIndexOutOfBoundsException: 10
        at uk.ac.ebi.interpro.scan.io.match.prints.PrintsMatchParser.parse(PrintsMatchParser.java:78)
        at uk.ac.ebi.interpro.scan.management.model.implementations.prints.ParsePrintsOutputStep.execute(ParsePrintsOutputStep.java:74)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
        at sun.reflect.GeneratedMethodAccessor66.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
         at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:180)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1071)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1063)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:960)
        at java.lang.Thread.run(Thread.java:724)
2015-11-08 02:26:18,156 [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:58] WARN - StepInstance 40 is being re-run following a failure.
2015-11-08 02:26:23,162 [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:192] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution.  All database activity rolled back.
java.lang.ArrayIndexOutOfBoundsException: 10
        at uk.ac.ebi.interpro.scan.io.match.prints.PrintsMatchParser.parse(PrintsMatchParser.java:78)
        at uk.ac.ebi.interpro.scan.management.model.implementations.prints.ParsePrintsOutputStep.execute(ParsePrintsOutputStep.java:74)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
        at sun.reflect.GeneratedMethodAccessor66.invoke(Unknown Source)
                at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
        at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:180)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1071)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1063)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:960)
        at java.lang.Thread.run(Thread.java:724)
2015-11-08 02:26:23,315 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 40 : Parse the output from FingerPrintScan for proteins 1 to 1 has failed irretrievably.  Available StackTraces follow.
2015-11-08 02:26:23,316 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2015-11-08 02:26:23,316 [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:107] ERROR - Exception thrown by Standalo
neBlackBoxMaster:
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:49)
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:290)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

[Pratyay]

Hi, can you guide me how to compile the src folder?

Many thanks!

Answer 1

[yangyongzhi2008]

I have resolved this error.

Find the "src" folder and compile it. Replace the "prints" under the bin folder with the compiled file.

This error has been resolved now.