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[interhelp #28135] java.lang.OutOfMemoryError: Java heap space #51

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I'm receiving an error message when I try to use a local installation of 
InterProScan v5.6-48.0. The full output is below, but briefly, the error is: 

java.lang.OutOfMemoryError: Java heap space

This occurs when I try to use a nucleotide FASTA file with 81K sequences (190Mb 
in size).  I've tried to increase the max memory by setting the -Xmx argument 
in the interproscan.sh file.  Currently I have it at 4048M.  Do I need to keep 
incrementing that value or is there something else that might be wrong?

The full ouput log (with path's removed) is below:  

Thanks,
Stephen

26/09/2014 07:37:16:962 Welcome to InterProScan-5.6-48.0
The Project/Cluster Run ID for this run is: CU_malus
26/09/2014 07:37:27:782 Running InterProScan v5 in CLUSTER mode...
Loading file Malus_x_domestica-CU_RNA_seq_genes-all.fa
26/09/2014 07:38:24:633 Running the following analyses:
[jobTIGRFAM-13.0,jobProDom-2006.1,jobPIRSF-2.84,jobPfamA-27.0,jobPrositeProfiles
-20.97,jobSMART-6.2,jobHAMAP-201311.27,jobPrositePatterns-20.97,jobPRINTS-42.0,j
obSuperFamily-1.75,jobCoils-2.2,jobGene3d-3.5.0]
Loading file 
/scratch/software/bioinfo/iprscan/temp/login1_20140926_073733582_ccn5/jobLoadNuc
leicAcidSequence/orfs.fasta
26/09/2014 07:45:30:095 Running the following analyses:
[jobTIGRFAM-13.0,jobProDom-2006.1,jobPIRSF-2.84,jobPfamA-27.0,jobPrositeProfiles
-20.97,jobSMART-6.2,jobHAMAP-201311.27,jobPrositePatterns-20.97,jobPRINTS-42.0,j
obSuperFamily-1.75,jobCoils-2.2,jobGene3d-3.5.0]
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.22014-09-29 02:25:00,773 
[org.hibernate.engine.loading.LoadContexts:132] WARN - fail-safe cleanup 
(collections) : 
org.hibernate.engine.loading.CollectionLoadContext@6bc2763d<rs=rs2777715: null>
2014-09-29 02:28:56,968 
[org.hibernate.engine.loading.CollectionLoadContext:348] WARN - On 
CollectionLoadContext#cleanup, localLoadingCollectionKeys contained [1] entries
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
    at org.h2.util.IOUtils.copy(IOUtils.java:161)
    at org.h2.util.IOUtils.copy(IOUtils.java:145)
    at org.h2.util.Utils.loadResource(Utils.java:537)
    at org.h2.util.Utils.getResource(Utils.java:509)
    at org.h2.message.DbException.<clinit>(DbException.java:38)
    at org.h2.command.Command.executeQuery(Command.java:195)
    at org.h2.jdbc.JdbcConnection.getQueryTimeout(JdbcConnection.java:708)
    at org.h2.jdbc.JdbcStatement.getQueryTimeout(JdbcStatement.java:532)
    at org.hibernate.jdbc.AbstractBatcher.closeQueryStatement(AbstractBatcher.java:299)
    at org.hibernate.jdbc.AbstractBatcher.closeQueryStatement(AbstractBatcher.java:234)
    at org.hibernate.loader.Loader.doQuery(Loader.java:854)
    at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:274)
    at org.hibernate.loader.Loader.loadCollection(Loader.java:2166)
    at org.hibernate.loader.collection.CollectionLoader.initialize(CollectionLoader.java:62)
    at org.hibernate.persister.collection.AbstractCollectionPersister.initialize(AbstractCollectionPersister.java:627)
    at org.hibernate.event.def.DefaultInitializeCollectionEventListener.onInitializeCollection(DefaultInitializeCollectionEventListener.java:83)
    at org.hibernate.impl.SessionImpl.initializeCollection(SessionImpl.java:1863)
    at org.hibernate.collection.AbstractPersistentCollection.forceInitialization(AbstractPersistentCollection.java:479)
    at org.hibernate.engine.StatefulPersistenceContext.initializeNonLazyCollections(StatefulPersistenceContext.java:900)
    at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:279)
    at org.hibernate.loader.Loader.doList(Loader.java:2533)
    at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2276)
    at org.hibernate.loader.Loader.list(Loader.java:2271)
    at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:452)
    at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:363)
    at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:196)
    at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1268)
    at org.hibernate.impl.QueryImpl.list(QueryImpl.java:102)
    at org.hibernate.ejb.QueryImpl.getResultList(QueryImpl.java:246)
    at uk.ac.ebi.interpro.scan.management.dao.StepInstanceDAOImpl.retrieveUnfinishedStepInstances(StepInstanceDAOImpl.java:97)
    at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Sourc
Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler 
in thread "AcException in thread "BrokerService[localhost] Task-2847" 
java.lang.OutOfMemoryError: Java heap space
r" java.lang.OutOfMemoryError: Java heap space
Exception in thread "BrokerService[localhost] Task-4831" 
java.lang.OutOfMemoryError: Java heap space
Exception in thread "pool-3-thread-1" java.lang.OutOfMemoryError: Java heap 
space
Loading file 
/scratch/software/bioinfo/iprscan/temp/login1_20140924_124326110_4tt/jobLoadNucl
eicAcidSequence/orfs.fasta
29/09/2014 16:53:47:924 Running the following analyses:
[jobTIGRFAM-13.0,jobProDom-2006.1,jobPIRSF-2.84,jobPfamA-27.0,jobPrositeProfiles
-20.97,jobSMART-6.2,jobHAMAP-201311.27,jobPrositePatterns-20.97,jobPRINTS-42.0,j
obSuperFamily-1.75,jobCoils-2.2,jobGene3d-3.5.0]
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.

Original issue reported on code.google.com by spfick...@gmail.com on 30 Sep 2014 at 2:23

GoogleCodeExporter commented 9 years ago

Original comment by Mr.Matth...@gmail.com on 30 Sep 2014 at 2:54

GoogleCodeExporter commented 9 years ago 
Dear Stephen,

Thank you for the email! 81k nucleotide sequences would take a very long time 
and use a lot of memory. I'd advise you to split your input into smaller chunks.

FAQ entry #10 has some more information about this...

https://code.google.com/p/interproscan/wiki/FAQ#10.How_to_analyse_a_huge_amount_
of_protein_sequences_%28%3E3000%29?

I hope that will help to solve your problem?

Regards,

Matthew
InterPro team

Original comment by Mr.Matth...@gmail.com on 30 Sep 2014 at 3:00

GoogleCodeExporter commented 9 years ago 
Ah, okay. I'll try that.   

Thanks.

Original comment by spfick...@gmail.com on 30 Sep 2014 at 4:00

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 14 Nov 2014 at 12:02