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8.7 years ago
grayapply2009
▴
280
I installed interproscan5 and tried to run the test fasta files with it. It works perfectly for protein fasta files but when I scan nucleotide sequences I got following errors:
Error Message:
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:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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.$Proxy96.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:180)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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:744)
Loading file /users/lei/Gray/interproscan-5.14-53.0/test1.fasta
23/07/2015 18:07:47:063 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]
2015-07-23 18:07:47,107 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 3 : Run GetOrf to predict open reading frames from nucleic acid sequence for proteins null to null has failed irretrievably. Available StackTraces follow.
2015-07-23 18:07:47,107 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2015-07-23 18:07:47,107 [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
what happens when you run: /users/lei/Gray/interproscan-5.14-53.0/bin/nucleotide/getorf ? Do you get the same error? Not sure why getorf should be linked against libmysqlclient. If the error persists or other bundled binaries break, I'd compile my own getorf (or whatever other binary) from emboss tools and change the configuration of the getorf path in the interproscan configuration file to the new binary.
Directly run getorf, I got this:
error while loading shared libraries: libmysqlclient.so.16: cannot open shared object file: No such file or directory
looks like the same error. Does it matter which version of emboss I install if I install emboss independently? or which version is compatible to interproscan5?
I think this link should help and try with the latest version first, https://code.google.com/p/interproscan/wiki/CompilingBinaries#EMBOSS_getorf, and https://code.google.com/p/interproscan/issues/detail?id=44
Seems like the bundled version of getorf is linked against libmysqlclient.so.16 with that exact version,
you can also check that using
ldd </pathto/>getorf | grep libmysqlclient, this will most likely show 'undef'.Now if you re-compile getorf with configure option
it should work, alternatively you could try to install the mysqlclient from your package system.
Great, it works. Thank you, Michael. Another question, for the lookup datbase, do I have to leave it run to run my interproscan after I add "precalculated.match.lookup.service.url=http://lookup:8080" to the properties?
Simple solution on Ubuntu:
Just install the debian version: sudo apt-get install emboss
then backup the getorf file: mv path_to_interpro/bin/nucleotide/getorf path_to_interpro/bin/nucleotide/getorf.bck ln -s /usr/bin/getopt path_to_interpro/bin/nucleotide/getorf
or setup the proper variables for the new local installation done in the first command: https://github.com/ebi-pf-team/interproscan/wiki/ScanNucleicAcidSeqs