problem with ncoils

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What steps will reproduce the problem?
1.  all my runs produce a problem
2.
3.

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

I get an error

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:82)
        at sun.reflect.GeneratedMethodAccessor66.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:318)
        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 $Proxy90.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanWorker.onMessage(AmqInterProScanWorker.java:96)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:561)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:499)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:467)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:325)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:263)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1059)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1051)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:948)
        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)
        ... 21 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)
        ... 24 more

What version of the product are you using? On what operating system?
interproscan5 and the operating sistem is ubuntu 64 bit

Please provide any additional information below.

I think that the problem is the ncoils software which is not able to run. I 
tested to run the software from the londer where the software is located in 
/programs/interproscan5/interproscan-5-RC1/bin/coils and it gives this error 
too: ./ncoils: No such file or directory

hope that you can help.

thanks

Original issue reported on code.google.com by luigi.fa...@gmail.com on 9 Jun 2012 at 1:40

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Yes - I had the same with RC1 - the ncoils binary is the same [32-bit] in both 
the 32- and 64-bit releases. I ended up compiling it (easy enough). There's a 
similar issue with bin/blast/2.2.6/blastall

Original comment by simon.po...@eaglegenomics.com on 8 Aug 2012 at 12:33

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Does the coils analysis work?

I've submitted a job using the three test sequcences that come with the ncoils 
'package'. All three produce predictions of some sort from ncoils direct, yet 
none produces any output when run through either RC1 or RC2 (with or without 
the EBI lookup).

Original comment by simon.po...@eaglegenomics.com on 9 Aug 2012 at 10:43

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If you're using ubuntu then rather than compiling it you can also install coils 
from package manager and copy the binary over the one that ships with ipr5

Original comment by martin...@gmail.com on 17 Sep 2012 at 2:34

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[deleted comment]

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Hi, just to confirm that the issue is still present in RC5.
downloading blastall and compiling it works fine.
But for coil, after compilation and replacement of the new binary there is 
still an error:
error: environment variable COILSDIR must be set
How are we suppose to modify the coils.c file?
N. Terrapon

Original comment by gandar...@gmail.com on 15 Mar 2013 at 2:08

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Hi all,
Thanks for reporting that issue. It is true, this one still occurs in RC5. But 
we are looking into that problem very soon and will keep you up-to-date.
Many Thanks,
Maxim

Original comment by Maxim.Sc...@gmail.com on 21 Mar 2013 at 10:05

• Changed state: Started

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Dear InterProScan users,

We have just added a page to our documentation on how to compile the binaries 
(including coils) used in Interproscan.

If you are getting an error after compiling and replacing the binary, you could 
try the following - instead of copying the binary to your ipr5 installtion, 
leave it where it is and update the following line in the 
interproscan.properties file to point to the binary:
binary.coils.path=

Hope this helps,
Craig

Original comment by newboycr...@gmail.com on 27 Mar 2013 at 2:52

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Original comment by Maxim.Sc...@gmail.com on 17 Apr 2013 at 9:39

• Changed state: Done

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Is there any documentation on how to compile binaries for blastall (2.2.6)?

Thanks,
Veronica

Original comment by vmgaia...@gmail.com on 25 Jun 2013 at 1:37

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Dear Veronica,

Thanks for pointing that out. I've just added a blastall installation section 
on the following page:
https://code.google.com/p/interproscan/wiki/CompilingBinaries#BLASTALL

Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 26 Jun 2013 at 8:38