Question: interproscan5 doesn't work for nucelotide sequences but works for protein sequences??
1
gravatar for grayapply2009
5.0 years ago by
grayapply2009210
United States
grayapply2009210 wrote:

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

interproscan • 2.8k views
ADD COMMENTlink modified 3.7 years ago by netbofia20 • written 5.0 years ago by grayapply2009210

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.

ADD REPLYlink written 5.0 years ago by Michael Dondrup47k

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?

ADD REPLYlink written 5.0 years ago by grayapply2009210
1

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

./configure --without-mysql

it should work, alternatively you could try to install the mysqlclient from your package system.

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by Michael Dondrup47k

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?

ADD REPLYlink written 5.0 years ago by grayapply2009210

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

ADD REPLYlink written 3.7 years ago by netbofia20
0
gravatar for netbofia
3.7 years ago by
netbofia20
netbofia20 wrote:

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

make a symlink::

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

ADD COMMENTlink written 3.7 years ago by netbofia20
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