[jobPfamA-26.0] fails

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Run interproscan.sh -aapl PfamA some.seq
2.
3.

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

13/05/2013 14:21:11 Welcome to InterProScan 5RC6
Running the following analyses:
[jobPfamA-26.0]
Running InterProScan v5 in STANDALONE mode...
Pre-calculated match lookup service DISABLED.  Please wait for match 
calculations to complete...
13/05/2013 14:22:36 38% completed
2013-05-13 14:22:42,359 
[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 parse 
temp/iq218_20130513_142132149_i72k/jobPfamA-26.0/000000000001_000000000004.raw.o
ut
    at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:77)
    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(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    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 sun.proxy.$Proxy94.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Thread.java:679)
Caused by: java.io.IOException: No locks available
    at sun.nio.ch.FileChannelImpl.lock0(Native Method)
    at sun.nio.ch.FileChannelImpl.lock(FileChannelImpl.java:887)
    at uk.ac.ebi.interpro.scan.io.model.GaValuesRetriever.loadMappingFromPropertiesFile(GaValuesRetriever.java:141)
    at uk.ac.ebi.interpro.scan.io.model.GaValuesRetriever.lazyInitialise(GaValuesRetriever.java:95)
    at uk.ac.ebi.interpro.scan.io.model.GaValuesRetriever.getSequenceGAForAccession(GaValuesRetriever.java:75)
    at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Pfam_A_Hmmer3Hmmer3ParserSupport.addMatch(Pfam_A_Hmmer3Hmmer3ParserSupport.java:96)
    at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Hmmer3SearchMatchParser.parse(Hmmer3SearchMatchParser.java:183)
    at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:66)
    ... 22 more
What version of the product are you using? On what operating system?

this is RC6 and is running on a Sun Grid Engine machine 

Please provide any additional information below.

Original issue reported on code.google.com by jizosa...@gmail.com on 13 May 2013 at 9:44

[GoogleCodeExporter]

Hi,

The problem you have concerns file locking on an NFS distribution. On some NFS 
installations file locking does not work, or doesn't work in the way we expect.

You should change the following nfs delay property value in 
interproscan.properties file 
    nfs.delay.milliseconds=0 

Let us know which value works for you as we are not able to reproduce this 
problem on our installation.

Best regards,
Gift
InterPro Team

Original comment by nuka....@gmail.com on 14 May 2013 at 10:09

[GoogleCodeExporter]

Thanks for the prompt response and specific suggestions. I am afraid that this 
didn't fix the problem though.

It was originally set at 0 I have tried 50, 500, 5000, 50000, and 500000. and 
this doesn't seem to help.

I am still getting the same error. Any other thoughts?

Thanks,

Original comment by jizosa...@gmail.com on 15 May 2013 at 12:14

[GoogleCodeExporter]

So it seems that the problem stemmed from having the application on an NSF 
mount. When I mount it in my cluster home directory, it runs fine.

Original comment by jizosa...@gmail.com on 22 May 2013 at 9:29

[GoogleCodeExporter]

The change for this is done now.

Original comment by nuka....@gmail.com on 6 Aug 2013 at 4:07

• Changed state: Fixed