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Anotation of a sequence of nucleic acid #13

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. I need do an anotation for nucleic acid
2. Running interproscan 5 
3. I use the next comand:  ./interproscan.sh -t n -i contigs.fa -f GFF3 -o 
contigs.fa.GFF3  

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

Welcome to InterProScan 5RC4
Running the following analyses:
[jobProDom-2006.1, jobPanther-7.2, jobGene3d-3.3.0, jobSMART-6.2, 
jobTIGRFAM-12.0, jobPfamA-26.0, jobSuperFamily-1.75, jobPrositePatterns-20.83, 
jobPRINTS-42.0, jobPIRSF-2.82, jobPrositeProfiles-20.83, jobHAMAP-201207.04, 
jobCoils-2.2]
Running InterProScan v5 in STANDALONE mode...
Available matches will be retrieved from the pre-calculated match lookup 
service.

Matches for any sequences that are not represented in the lookup service will 
be calculated locally.
2013-01-11 13:17:28,592 
[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: Couldn't find nucleotide sequence by the 
following cross reference: NODE_11386_length_690_cov_9
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.createAndPersistNewORFs(ProteinLoader.java:293)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.persistBatch(ProteinLoader.java:182)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.addProteinToBatch(ProteinLoader.java:162)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.lookupProteins(ProteinLoader.java:140)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.storeAll(ProteinLoader.java:254)
    at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:104)
    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 $Proxy90.loadSequences(Unknown Source)
    at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:151)
    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 $Proxy94.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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)
2013-01-11 13:17:28,771 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:44] WARN - 
StepInstance 2 is being re-run following a failure.
Available matches will be retrieved from the pre-calculated match lookup 
service.

Matches for any sequences that are not represented in the lookup service will 
be calculated locally.
2013-01-11 13:51:52,836 
[uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener:106] ERROR - Execution 
thrown when attempting to executeInTransaction the StepExecution.  All database 
activity rolled back.
javax.persistence.PersistenceException: 
org.hibernate.PersistentObjectException: detached entity passed to persist: 
uk.ac.ebi.interpro.scan.model.Protein
    at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1214)
    at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1147)
    at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1153)
    at org.hibernate.ejb.AbstractEntityManagerImpl.persist(AbstractEntityManagerImpl.java:678)
    at sun.reflect.GeneratedMethodAccessor46.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:240)
    at $Proxy41.persist(Unknown Source)
    at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insertNewProteins(ProteinDAOImpl.java:253)
    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 $Proxy42.insertNewProteins(Unknown Source)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.persistBatch(ProteinLoader.java:178)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.addProteinToBatch(ProteinLoader.java:162)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.lookupProteins(ProteinLoader.java:140)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.storeAll(ProteinLoader.java:254)
    at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:104)
    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 $Proxy90.loadSequences(Unknown Source)
    at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:151)
    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 $Proxy94.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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: org.hibernate.PersistentObjectException: detached entity passed to 
persist: uk.ac.ebi.interpro.scan.model.Protein
    at org.hibernate.event.def.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:127)
    at org.hibernate.event.def.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:61)
    at org.hibernate.impl.SessionImpl.firePersist(SessionImpl.java:808)
    at org.hibernate.impl.SessionImpl.persist(SessionImpl.java:782)
    at org.hibernate.impl.SessionImpl.persist(SessionImpl.java:786)
    at org.hibernate.ejb.AbstractEntityManagerImpl.persist(AbstractEntityManagerImpl.java:672)
    ... 56 more
2013-01-11 13:51:52,892 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL 
- Analysis step 2 : Load proteins from a fasta file generated by GetOrf and 
create required JobInstance objects.  Also creates OpenReadingFrame records to 
connect the proteins to the NucleicAcid records. for proteins null to null has 
failed irretrievably.  Available StackTraces follow.
2013-01-11 13:51:52,892 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL 
- The JVM will now exit with a non-zero exit status.

What version of the product are you using? On what operating system?

Interproscan 5. Ubuntu 12.04
Please provide any additional information below.

Original issue reported on code.google.com by kelly.bo...@gmail.com on 14 Jan 2013 at 2:18

GoogleCodeExporter commented 9 years ago 
Hi Kelly,

We will have a look into that and will come back as soon as we found a 
solution. My guess is, that your nucleotide sequence header OR identifier 
(NODE_11386_length_690_cov_9) is in an unsupported format. As we use an 
external tool for protein prediction (EMBOSS getORF) the supported format is 
more restricted, but I can not be more precisely here at the moment.

Thanks for getting in contact.
Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 17 Jan 2013 at 10:46

GoogleCodeExporter commented 9 years ago 
Dear Kelly,

The current InterProScan 5 definitely has issues in parsing FASTA headers of 
nucleotide sequence. We are now aware of that and we will try to fix that 
probably for the next release after RC5.

For the moment I can just say underscores '_' and dots '.' in the FASTA header 
of nucleic sequences could cause InterProScan to die. 

Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 27 Feb 2013 at 12:48

GoogleCodeExporter commented 9 years ago 
Dear Maxim, 

I also run interproscan.5RC6 for nucleotide seq. I'. getting these error;

Error output from binary:
Error: File bin/nucleotide/getorf.acd line 1:(getorf) Attribute 'relations' 
unknown

FATAL- Analysis step 4 : run getorf to predict open reading frames from nucleic 
acid sequence for proteins null to null has failed irretrievably

Please help

Regards,
Syikin

Original comment by SnF310...@gmail.com on 21 Jun 2013 at 2:44

GoogleCodeExporter commented 9 years ago 
Dear Syikin,

The 2 error lines you see are produced by the EMBOSS getorf binary file itself 
and not from InterProScan 5 (I5). Therefore it might be question to the EMBOSS 
developers (http://emboss.sourceforge.net/).
We never came across such an error. Maybe a new clean installation of the 
EMBOSS package and then pointing InterProScan 5 to that new getorf binary file 
could solve the problem, but I am not sure about that. You can change the path 
of the getorf binary file inside the properties file (interproscan.properties), 
which you will find in the same directory as the start script interproscan.sh.

Could I also ask you a couple of question? On which operating system do you run 
I5? What was the command and have you changed anything in the I5 properties 
file or the start script?

Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 21 Jun 2013 at 11:24

GoogleCodeExporter commented 9 years ago 
Hi,

I do not know if anyone found a quick fix to this problem. I recently installed 
InterProScan 5RC7 on my laptop (Ubuntu 12.04 , x86_64 GNU/Linux) and noticed 
that you still get the same problem even when there is no "." or "_" in the 
FASTA header.
I was able to bypass this problem by changing to:
binary.getorf.path=/usr/bin/getorf

in the property file as suggested earlier. So far, it is working well.

Many thanks

KSM

Original comment by ksmba...@gmail.com on 24 Sep 2013 at 9:30

GoogleCodeExporter commented 9 years ago 
Hi KSM,

Just to avoid confusion for you and any else who might read this, I would like 
to point out, that the original submitted problem "Anotation of a sequence of 
nucleic acid", submitted by Kelly has nothing to do with your problem as far as 
I can see. Just to be clear, your problem is not caused by the fact that the 
FASTA header is in an unexpected format.

The issue you described has more to do with the installation of the EMBOSS 
getorf package (described in Issue 11). And I am glad that you fixed that by 
pointing to your local installation. So just keep your configuration as it is.

Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 24 Sep 2013 at 10:22

GoogleCodeExporter commented 9 years ago 
Hi all,

Going back to Kelly's originally submitted issue. This should be fixed now. The 
fix will be part of the official release of InterProScan 5, which will happen 
soon.

Best wishes,
Maxim

Original comment by Maxim.Sc...@gmail.com on 24 Sep 2013 at 10:27

GoogleCodeExporter commented 9 years ago 
hello all,
we are using interproscan-5-RC6 for aligning the protein sequence. Whenever we 
give protein sequence file it shows the following error:

2013-10-01 19:35:26,719 
[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.IllegalArgumentException: 'ProteinXref' must not be null
        at uk.ac.ebi.interpro.scan.model.Protein.addCrossReference(Protein.java:439)
        at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadProteinFastaFile.addToMoleculeCollection(LoadProteinFastaFile.java:35)
        at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:87)
        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 $Proxy90.loadSequences(Unknown Source)
        at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:154)
        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: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 $Proxy94.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$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:662)

Can you please guide us what we are doing wrong? Is there some database/model 
we are missing?

If we use DNA sequence as input file it runs fine without any error.

Thanks and Regards,
Madhu

Original comment by mmadhubi...@gmail.com on 1 Oct 2013 at 2:35