Problem running interproscan-5.14-53.0 for protein sequences
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Entering edit mode
8.7 years ago
mirzagold66 ▴ 20

Hello,

I am using the standalone interproscan-5.14-53.0. I could run the given test_proteins file successfully however, when I am trying to run my protein sequences, it gives the following error, please help me out as I am new to linux or say analysis/ software using command prompt:

Welcome to InterProScan-5.14-53.0
21/08/2015 12:32:23:643 Running InterProScan v5 in STANDALONE mode...
Loading file /home/smarla/my_interproscan/interproscan-5.14-53.0/SnG_1.txt
21/08/2015 12:32:28:606 Running the following analyses:
[jobProDom-2006.1,jobHAMAP,jobSMART-6.2,jobSuperFamily-1.75,jobPRINTS-42.0,jobPanther-9.0,jobGene3d-3.5.0,jobPIRSF-3.01,jobPfam,jobPrositeProfiles,jobTIGRFAM-15.0,jobPrositePatterns,jobCoils-2.2]
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.
21/08/2015 12:33:53:067 26% completed
2015-08-21 12:34:30,124 [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.GeneratedMethodAccessor64.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:622)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:180)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:701)
2015-08-21 12:34:30,208 [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:58] WARN - StepInstance 54 is being re-run following a failure.
21/08/2015 12:34:41:177 51% completed
2015-08-21 12:34:50,489 [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.GeneratedMethodAccessor64.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:622)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:180)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:701)
2015-08-21 12:34:50,596 [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:58] WARN - StepInstance 54 is being re-run following a failure.
21/08/2015 12:34:52:055 79% completed
2015-08-21 12:34:56,321 [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.GeneratedMethodAccessor64.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:622)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:180)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:701)
2015-08-21 12:34:56,454 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 54 : Parse the output from FingerPrintScan for proteins 1 to 6 has failed irretrievably.  Available StackTraces follow.
2015-08-21 12:34:56,454 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2015-08-21 12:34:56,454 [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:107] 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: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
smarla@smarla-HP-Z400-Workstation:~/my_interproscan/interproscan-5.14-53.0$

The error log file is always empty!

OTHER INFORMATION: I am using-

  1. OS: Linux Ubuntu SMP Tue Sep 2 05:02:14 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

  2. Ubuntu-version:

    LSB Version:   core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch

Distributor ID:    Ubuntu
Description:   Ubuntu 12.04.5 LTS
Release:   12.04
Codename:  precise

  3. java version: 1.6.0_35 OpenJDK Runtime Environment (IcedTea6 1.13.7) (6b35-1.13.7-1ubuntu0.12.04.2) (OpenJDK 64-Bit Server VM (build 23.25-b01, mixed mode))

  4. Python 2.7.3
interproscan • 5.0k views
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1
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-appl PRINTS

didn't work

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1
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what could be the possible reason & solution

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0
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This could be a bug or a problem with the installation (check if prints is working), you should ask interproscan support directly at interhelp@ebi.ac.uk

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Thank u for your reply. I have already sent a mail to those people with all the details.

The installation was successful. What do you mean by "check if prints is working" I mean, how to check this?

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There is a version of PRINTS bundled with the interproscan programs, you can find it i think under interproscan-5.14-53.0/bin with the other binaries. Maybe it fails silently, you could at least try to execute the PRINTS executable in the shell and see if it can be executed and displays its help message.

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I interproscan team responded. My problem is almost solved. Thank you.

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Hi @mirzogold66, would you mind saying how you solved the problem? I am having the same issue :(

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7.8 years ago
Matt ▴ 10

From https://github.com/ebi-pf-team/interproscan/wiki/CompilingBinaries "The binaries that we distribute with InterProScan should work on most linux systems. However, in some cases they may not work on a particular system. If this happens you need to compile the binary on your own system in order for it to work."

That wiki page also has instructions on how to compile the various binaries. This particular error was related to the bin/prints/fingerPRINTScan binary file used by the PRINTS analysis.

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