BatchingInterceptor is trying to resume a transaction that is in prepared state

When the Spring AppContext starts, the EntityManager bean initializes, which inits Hibernate Search, and this one inits Infinispan's Lucene Directory.
The Directory initializes Lucene Index and closes it. In this moment, org.infinispan.batch.BatchContainer ends the batch, which was running a micro transactions, so it commits the transaction.
The JTA sends a Prepare message to Infinispan XA. org.infinispan.interceptors.BatchingInterceptor receives the Prepare command and checks if there is an ongoing transaction. The transactionManager returns null because the transaction is not active but in prepare phase, so the BatchingInterceptor believes that the transaction is suspended and tries to resume it.

Exception does not seem to happen if Infinispan uses JTA synchronization instead of XAresource, although in that case there is no recovery.

Here is the stack trace:
10:01:51,964 ERROR TransactionCoordinator:154 - Error while processing prepare
java.lang.IllegalStateException: Transaction no longer active
at com.atomikos.icatch.imp.TxTerminatedStateHandler.addSubTxAwareParticipant(TxTerminatedStateHandler.java:95)
at com.atomikos.icatch.imp.CompositeTransactionImp.addSubTxAwareParticipant(CompositeTransactionImp.java:260)
at com.atomikos.icatch.imp.BaseTransactionManager.restoreThreadMappings(BaseTransactionManager.java:168)
at com.atomikos.icatch.imp.BaseTransactionManager.resume(BaseTransactionManager.java:393)
at com.atomikos.icatch.jta.TransactionManagerImp.resume(TransactionManagerImp.java:399)
at com.atomikos.icatch.jta.UserTransactionManager.resume(UserTransactionManager.java:204)
at org.infinispan.interceptors.BatchingInterceptor.handleDefault(BatchingInterceptor.java:54)
at org.infinispan.commands.AbstractVisitor.visitPrepareCommand(AbstractVisitor.java:113)
at org.infinispan.commands.tx.PrepareCommand.acceptVisitor(PrepareCommand.java:131)
at org.infinispan.interceptors.InterceptorChain.invoke(InterceptorChain.java:345)
at org.infinispan.transaction.TransactionCoordinator.prepare(TransactionCoordinator.java:140)
at org.infinispan.transaction.TransactionCoordinator.prepare(TransactionCoordinator.java:122)
at org.infinispan.transaction.xa.TransactionXaAdapter.commit(TransactionXaAdapter.java:122)
at com.atomikos.datasource.xa.XAResourceTransaction.commit(XAResourceTransaction.java:784)
at com.atomikos.icatch.imp.CommitMessage.send(CommitMessage.java:73)
at com.atomikos.icatch.imp.PropagationMessage.submit(PropagationMessage.java:111)
at com.atomikos.icatch.imp.Propagator$PropagatorThread.run(Propagator.java:87)
at com.atomikos.icatch.imp.Propagator.submitPropagationMessage(Propagator.java:66)
at com.atomikos.icatch.imp.CoordinatorStateHandler.commit(CoordinatorStateHandler.java:614)
at com.atomikos.icatch.imp.ActiveStateHandler.commit(ActiveStateHandler.java:289)
at com.atomikos.icatch.imp.CoordinatorImp.commit(CoordinatorImp.java:863)
at com.atomikos.icatch.imp.CoordinatorImp.terminate(CoordinatorImp.java:1157)
at com.atomikos.icatch.imp.CompositeTerminatorImp.commit(CompositeTerminatorImp.java:92)
at com.atomikos.icatch.jta.TransactionImp.commit(TransactionImp.java:236)
at com.atomikos.icatch.jta.TransactionManagerImp.commit(TransactionManagerImp.java:464)
at com.atomikos.icatch.jta.UserTransactionManager.commit(UserTransactionManager.java:175)
at org.infinispan.batch.BatchContainer.resolveTransaction(BatchContainer.java:123)
at org.infinispan.batch.BatchContainer.endBatch(BatchContainer.java:105)
at org.infinispan.batch.BatchContainer.endBatch(BatchContainer.java:86)
at org.infinispan.CacheImpl.endBatch(CacheImpl.java:577)
at org.infinispan.lucene.InfinispanIndexOutput.close(InfinispanIndexOutput.java:211)
at org.apache.lucene.store.ChecksumIndexOutput.close(ChecksumIndexOutput.java:61)
at org.apache.lucene.index.SegmentInfos.finishCommit(SegmentInfos.java:901)
at org.apache.lucene.index.IndexWriter.finishCommit(IndexWriter.java:3516)
at org.apache.lucene.index.IndexWriter.commitInternal(IndexWriter.java:3506)
at org.apache.lucene.index.IndexWriter.closeInternal(IndexWriter.java:1882)
at org.apache.lucene.index.IndexWriter.close(IndexWriter.java:1825)
at org.apache.lucene.index.IndexWriter.close(IndexWriter.java:1789)
at org.hibernate.search.store.impl.DirectoryProviderHelper.initializeIndexIfNeeded(DirectoryProviderHelper.java:160)
at org.hibernate.search.infinispan.impl.InfinispanDirectoryProvider.start(InfinispanDirectoryProvider.java:88)
at org.hibernate.search.indexes.impl.DirectoryBasedIndexManager.initialize(DirectoryBasedIndexManager.java:93)
at org.hibernate.search.indexes.impl.IndexManagerHolder.createDirectoryManager(IndexManagerHolder.java:193)
at org.hibernate.search.indexes.impl.IndexManagerHolder.buildEntityIndexBinding(IndexManagerHolder.java:113)
at org.hibernate.search.spi.SearchFactoryBuilder.initDocumentBuilders(SearchFactoryBuilder.java:373)
at org.hibernate.search.spi.SearchFactoryBuilder.buildNewSearchFactory(SearchFactoryBuilder.java:224)
at org.hibernate.search.spi.SearchFactoryBuilder.buildSearchFactory(SearchFactoryBuilder.java:142)
at org.hibernate.search.event.impl.FullTextIndexEventListener.initialize(FullTextIndexEventListener.java:129)
at org.hibernate.search.hcore.impl.HibernateSearchIntegrator.integrate(HibernateSearchIntegrator.java:82)
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:294)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1737)
at org.hibernate.ejb.EntityManagerFactoryImpl.<init>(EntityManagerFactoryImpl.java:84)
at org.hibernate.ejb.Ejb3Configuration.buildEntityManagerFactory(Ejb3Configuration.java:904)
at org.hibernate.ejb.Ejb3Configuration.buildEntityManagerFactory(Ejb3Configuration.java:889)
at org.hibernate.ejb.HibernatePersistence.createContainerEntityManagerFactory(HibernatePersistence.java:73)
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:257)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:310)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor.findDefaultEntityManagerFactory(PersistenceAnnotationBeanPostProcessor.java:530)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor.findEntityManagerFactory(PersistenceAnnotationBeanPostProcessor.java:496)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor$PersistenceElement.resolveEntityManager(PersistenceAnnotationBeanPostProcessor.java:657)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor$PersistenceElement.getResourceToInject(PersistenceAnnotationBeanPostProcessor.java:630)
at org.springframework.beans.factory.annotation.InjectionMetadata$InjectedElement.inject(InjectionMetadata.java:150)
at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:87)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor.postProcessPropertyValues(PersistenceAnnotationBeanPostProcessor.java:339)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1106)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:585)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:384)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:283)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:111)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4521)
at org.apache.catalina.core.StandardContext$1.call(StandardContext.java:5004)
at org.apache.catalina.core.StandardContext$1.call(StandardContext.java:4999)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)