Dear Team,
I run Illumina plugin and had error: "Java heap space". I have increased
CATALINA OPTS=-Xmx2048m, however now I have the garbage collector problem:
"Error: GC overhead limit exceeded"
View job -- Run plugin: Illumina raw data importer
java.lang.OutOfMemoryError: GC overhead limit exceeded
at org.hibernate.engine.EntityEntry.getEntityKey(EntityEntry.java:182)
at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:198)
at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898)
at org.hibernate.loader.Loader.loadSingleRow(Loader.java:327)
at
org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:254)
at org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:123)
at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:66)
at net.sf.basedb.core.RawDataBatcher.<init>(RawDataBatcher.java:263)
at net.sf.basedb.core.RawDataBatcher.getNew(RawDataBatcher.java:104)
at net.sf.basedb.core.RawBioAssay.getRawDataBatcher(RawBioAssay.java:1119)
at
net.sf.basedb.plugins.IlluminaRawDataImporter.beginData(IlluminaRawDataImporter.java:520)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:691)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
at java.lang.Thread.run(Thread.java:636)
Did I gave too much memory?
Regards,
Irina
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