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InterProScan 5RC6 with -appl Coils executeInTransaction error #23

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.
./interproscan.sh -appl Coils -i test_proteins.fasta -f tsv

What is the expected output? What do you see instead?

24/06/2013 12:28:52 Welcome to InterProScan 5RC6
Running the following analyses:
[jobCoils-2.2]
Running InterProScan v5 in STANDALONE mode...
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.
2013-06-24 12:29:52,424 
[uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener:106] ERROR - Execution 
thrown when attempting to executeInTransaction the StepExecution.  All database 
activity rolled back.
java.lang.IllegalStateException: IOException thrown when attempting to run 
binary
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:84)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Unknown Source)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, 
No such file or directory
    at java.lang.ProcessBuilder.start(Unknown Source)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
    ... 22 more
Caused by: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(Unknown Source)
    at java.lang.ProcessImpl.start(Unknown Source)
    ... 25 more
24/06/2013 12:29:52 29% completed
2013-06-24 12:29:52,786 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:48] WARN - 
StepInstance 3 is being re-run following a failure.
2013-06-24 12:29:52,816 
[uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener:106] ERROR - Execution 
thrown when attempting to executeInTransaction the StepExecution.  All database 
activity rolled back.
java.lang.IllegalStateException: IOException thrown when attempting to run 
binary
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:84)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Unknown Source)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, 
No such file or directory
    at java.lang.ProcessBuilder.start(Unknown Source)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
    ... 22 more
Caused by: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(Unknown Source)
    at java.lang.ProcessImpl.start(Unknown Source)
    ... 25 more
2013-06-24 12:29:53,176 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:48] WARN - 
StepInstance 3 is being re-run following a failure.
2013-06-24 12:29:53,204 
[uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener:106] ERROR - Execution 
thrown when attempting to executeInTransaction the StepExecution.  All database 
activity rolled back.
java.lang.IllegalStateException: IOException thrown when attempting to run 
binary
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:84)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Unknown Source)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, 
No such file or directory
    at java.lang.ProcessBuilder.start(Unknown Source)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
    ... 22 more
Caused by: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(Unknown Source)
    at java.lang.ProcessImpl.start(Unknown Source)
    ... 25 more
2013-06-24 12:29:53,554 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL 
- Analysis step 3 : Run fingerprintscan Binary for selected proteins for 
proteins 1 to 4 has failed irretrievably.  Available StackTraces follow.
2013-06-24 12:29:53,559 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL 
- The JVM will now exit with a non-zero exit status.

What version of the product are you using? On what operating system?
InterProScan 5RC6 on Ubuntu 12.04.1 LTS - x64
java version "1.7.0_25"

I don't know if I'm doing anything wrong, but I've tested -appl 
TIGRFAM,PIRSF,ProDom,Panther,SMART,PrositeProfiles,HAMAP,PfamA,PrositePatterns,P
RINTS,SuperFamily,Gene3d and they all worked fine.

Thanks!

Original issue reported on code.google.com by vmgaia...@gmail.com on 24 Jun 2013 at 12:47

GoogleCodeExporter commented 9 years ago 
The binaries that we distribute with InterProScan should work for 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.

You will find further information on how to do that here:
http://code.google.com/p/interproscan/wiki/CompilingBinaries#Ncoils

Original comment by Maxim.Sc...@gmail.com on 24 Jun 2013 at 2:21

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 5 Nov 2013 at 12:22