[interhelp #47530] Problems

[GoogleCodeExporter]

03/07/2015 16:31:08:619 Welcome to InterProScan-5.13-52.0
03/07/2015 16:31:32:982 Running InterProScan v5 in STANDALONE mode...
2015-07-03 16:31:40,603 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:156] 
ERROR - Command line failed with exit code: 127
Command: bin/nucleotide/getorf -sf pearson -sequence 
/home/bruna/Downloads/interproscan-5.13-52.0/../pequeno.fasta -outseq 
/home/bruna/Downloads/interproscan-5.13-52.0/temp/bruna-POS-ECIG41BS_20150703_16
3132981_eeg7//jobLoadNucleicAcidSequence/orfs.fasta -minsize 50 
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: 
libmysqlclient.so.16: cannot open shared object file: No such file or directory

2015-07-03 16:31:40,610 
[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.IllegalStateException: Command line failed with exit code: 127
Command: bin/nucleotide/getorf -sf pearson -sequence 
/home/bruna/Downloads/interproscan-5.13-52.0/../pequeno.fasta -outseq 
/home/bruna/Downloads/interproscan-5.13-52.0/temp/bruna-POS-ECIG41BS_20150703_16
3132981_eeg7//jobLoadNucleicAcidSequence/orfs.fasta -minsize 50 
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: 
libmysqlclient.so.16: cannot open shared object file: No such file or directory

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:158)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    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:662)
Loading file /home/bruna/Downloads/interproscan-5.13-52.0/../pequeno.fasta
03/07/2015 16:31:40:662 Running the following analyses:
[jobHAMAP,jobProDom-2006.1,jobPIRSF-3.01,jobPfamA-27.0,jobSMART-6.2,jobPrositePr
ofiles,jobTIGRFAM-15.0,jobPRINTS-42.0,jobSuperFamily-1.75,jobPrositePatterns,job
Coils-2.2,jobGene3d-3.5.0]
2015-07-03 16:31:40,710 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL 
- Analysis step 4 : Run GetOrf to predict open reading frames from nucleic acid 
sequence for proteins null to null has failed irretrievably.  Available 
StackTraces follow.
2015-07-03 16:31:40,714 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL 
- The JVM will now exit with a non-zero exit status.
2015-07-03 16:31:40,714 
[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:261)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. 
Check the log file for details

Versions:
Linux Mint

Original issue reported on code.google.com by bzamit...@gmail.com on 3 Jul 2015 at 7:33

• Merged into: #68

[GoogleCodeExporter]

Original comment by Mr.Matth...@gmail.com on 21 Jul 2015 at 1:09

• Changed title: [interhelp #47530] Problems

[GoogleCodeExporter]

Original comment by Mr.Matth...@gmail.com on 27 Jul 2015 at 1:38

• Changed state: Duplicate

[GoogleCodeExporter]

Hi:
In my case (ubuntu-12.04.5 and interproscan-5.14-53.0) the problem was the 
getorf version that comes with interproscan package, but I had my own getorf on 
the system (because I installed emboss [sudo apt-get install emboss])

If you have emboss, use this command to locate the getorf path:
>whereis getorf
(in my case /usr/bin/getorf)

Then, go the interproscan home (where you unzipped/installed the program) and 
enter to this internal directory:
>cd bin/nucleotide

and move the old inteproscan getorf to getorf.bak
>mv getorf getorf.bak

Finally, create a symbolic link to your "system" getorf
>ln -s /usr/bin/getorf .

After this, the program run without the "127" problem

good luck!

Original comment by jomal...@gmail.com on 18 Aug 2015 at 8:30

[GoogleCodeExporter]

...or just change the path to the local getorf in the file 
"interproscan.properties".

binary.getorf.path=

Cheers

Original comment by jomal...@gmail.com on 18 Aug 2015 at 8:42