"Too many open files" error in large runs (again)

Windup Execution failed due to: Error encountered while evaluating rule: .addRule().perform(ParseJavaSource).withId("AnalyzeJavaFilesRuleProvider_1")
  From: org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider loaded from ModuleClassLoader for Module "org.jboss.windup.rules.apps.windup-rules-java:2.6.0-SNAPSHOT_1ad8b599-46fd-4c82-9cd6-c026fe4e07bf" from AddonModuleLoader
  Defined in: org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider.getConfiguration(AnalyzeJavaFilesRuleProvider.java:101)
org.jboss.windup.util.exception.WindupException: Error encountered while evaluating rule: .addRule().perform(ParseJavaSource).withId("AnalyzeJavaFilesRuleProvider_1")
  From: org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider loaded from ModuleClassLoader for Module "org.jboss.windup.rules.apps.windup-rules-java:2.6.0-SNAPSHOT_1ad8b599-46fd-4c82-9cd6-c026fe4e07bf" from AddonModuleLoader
  Defined in: org.jboss.windup.rules.apps.java.scan.provider.AnalyzeJavaFilesRuleProvider.getConfiguration(AnalyzeJavaFilesRuleProvider.java:101)
        at org.jboss.windup.config.RuleSubset.perform(RuleSubset.java:344)
        at org.jboss.windup.exec.WindupProcessorImpl.execute(WindupProcessorImpl.java:152)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.jboss.forge.furnace.proxy.ClassLoaderInterceptor$1.call(ClassLoaderInterceptor.java:87)
        at org.jboss.forge.furnace.util.ClassLoaders.executeIn(ClassLoaders.java:42)
        at org.jboss.forge.furnace.proxy.ClassLoaderInterceptor.invoke(ClassLoaderInterceptor.java:103)
        at org.jboss.windup.exec.WindupProcessorImpl_$$_javassist_15853e78-ca2a-404c-ba60-11ece51ddb6b.execute(WindupProcessorImpl_$$_javassist_15853e78-ca2a-404c-ba60-11ece51ddb6b.java)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.jboss.forge.furnace.proxy.ClassLoaderAdapterCallback$2.call(ClassLoaderAdapterCallback.java:123)
        at org.jboss.forge.furnace.util.ClassLoaders.executeIn(ClassLoaders.java:42)
        at org.jboss.forge.furnace.proxy.ClassLoaderAdapterCallback.invoke(ClassLoaderAdapterCallback.java:96)
        at org.jboss.windup.exec.WindupProcessor_$$_javassist_37f87ae3-a50e-4cfa-a0d7-594a903aa15c.execute(WindupProcessor_$$_javassist_37f87ae3-a50e-4cfa-a0d7-594a903aa15c.java)
        at org.jboss.windup.bootstrap.commands.windup.RunWindupCommand.runWindup(RunWindupCommand.java:264)
        at org.jboss.windup.bootstrap.commands.windup.RunWindupCommand.execute(RunWindupCommand.java:75)
        at org.jboss.windup.bootstrap.Bootstrap.executePhase(Bootstrap.java:308)
        at org.jboss.windup.bootstrap.Bootstrap.run(Bootstrap.java:171)
        at org.jboss.windup.bootstrap.Bootstrap.main(Bootstrap.java:97)
Caused by: com.thinkaurelius.titan.core.TitanException: Could not commit transaction due to exception during persistence
        at com.thinkaurelius.titan.graphdb.transaction.StandardTitanTx.commit(StandardTitanTx.java:1348)
        at com.thinkaurelius.titan.graphdb.blueprints.TitanBlueprintsGraph.commit(TitanBlueprintsGraph.java:60)
        at org.jboss.windup.config.RuleSubset.perform(RuleSubset.java:306)
        ... 22 more
Caused by: com.thinkaurelius.titan.core.TitanException: Could not execute operation due to backend exception
        at com.thinkaurelius.titan.diskstorage.util.BackendOperation.execute(BackendOperation.java:44)
        at com.thinkaurelius.titan.diskstorage.keycolumnvalue.cache.CacheTransaction.persist(CacheTransaction.java:86)
        at com.thinkaurelius.titan.diskstorage.keycolumnvalue.cache.CacheTransaction.flushInternal(CacheTransaction.java:140)
        at com.thinkaurelius.titan.diskstorage.keycolumnvalue.cache.CacheTransaction.commit(CacheTransaction.java:197)
        at com.thinkaurelius.titan.diskstorage.BackendTransaction.commitStorage(BackendTransaction.java:117)
        at com.thinkaurelius.titan.graphdb.database.StandardTitanGraph.commit(StandardTitanGraph.java:670)
        at com.thinkaurelius.titan.graphdb.transaction.StandardTitanTx.commit(StandardTitanTx.java:1337)
        ... 24 more
Caused by: com.thinkaurelius.titan.diskstorage.PermanentBackendException: Permanent failure in storage backend
        at com.thinkaurelius.titan.diskstorage.berkeleyje.BerkeleyJEKeyValueStore.insert(BerkeleyJEKeyValueStore.java:206)
        at com.thinkaurelius.titan.diskstorage.berkeleyje.BerkeleyJEKeyValueStore.insert(BerkeleyJEKeyValueStore.java:183)
        at com.thinkaurelius.titan.diskstorage.berkeleyje.BerkeleyJEStoreManager.mutateMany(BerkeleyJEStoreManager.java:193)
        at com.thinkaurelius.titan.diskstorage.keycolumnvalue.keyvalue.OrderedKeyValueStoreManagerAdapter.mutateMany(OrderedKeyValueStoreManagerAdapter.java:100)
        at com.thinkaurelius.titan.diskstorage.keycolumnvalue.cache.CacheTransaction$1.call(CacheTransaction.java:89)
        at com.thinkaurelius.titan.diskstorage.keycolumnvalue.cache.CacheTransaction$1.call(CacheTransaction.java:86)
        at com.thinkaurelius.titan.diskstorage.util.BackendOperation.executeDirect(BackendOperation.java:56)
        at com.thinkaurelius.titan.diskstorage.util.BackendOperation.execute(BackendOperation.java:42)
        ... 30 more
Caused by: com.sleepycat.je.EnvironmentFailureException: (JE 5.0.73) Environment must be closed, caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 5.0.73) /tmp/Windup/resClfy/graph/titangraph java.io.FileNotFoundException: /tmp/Windup/resClfy/graph/titangraph/00000019.jdb (Too many open files) LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed. fetchTarget of 0x26b/0x35bb56 parent IN=90744 IN class=com.sleepycat.je.tree.IN lastFullVersion=0x285/0x1f8c6d lastLoggedVersion=0x285/0x1f8c6d parent.getDirty()=false state=0
        at com.sleepycat.je.EnvironmentFailureException.wrapSelf(EnvironmentFailureException.java:196)
        at com.sleepycat.je.dbi.EnvironmentImpl.checkIfInvalid(EnvironmentImpl.java:1512)
        at com.sleepycat.je.Database.checkEnv(Database.java:1884)
        at com.sleepycat.je.Database.put(Database.java:1164)
        at com.thinkaurelius.titan.diskstorage.berkeleyje.BerkeleyJEKeyValueStore.insert(BerkeleyJEKeyValueStore.java:194)
        ... 37 more
Caused by: com.sleepycat.je.EnvironmentFailureException: Environment invalid because of previous exception: (JE 5.0.73) /tmp/Windup/resClfy/graph/titangraph java.io.FileNotFoundException: /tmp/Windup/resClfy/graph/titangraph/00000019.jdb (Too many open files) LOG_FILE_NOT_FOUND: Log file missing, log is likely invalid. Environment is invalid and must be closed. fetchTarget of 0x26b/0x35bb56 parent IN=90744 IN class=com.sleepycat.je.tree.IN lastFullVersion=0x285/0x1f8c6d lastLoggedVersion=0x285/0x1f8c6d parent.getDirty()=false state=0
        at com.sleepycat.je.log.LogManager.getLogEntryHandleFileNotFound(LogManager.java:862)
        at com.sleepycat.je.log.LogManager.getEntryHandleFileNotFound(LogManager.java:1121)
        at com.sleepycat.je.tree.BINDelta.reconstituteBIN(BINDelta.java:141)
        at com.sleepycat.je.log.entry.BINDeltaLogEntry.getIN(BINDeltaLogEntry.java:53)
        at com.sleepycat.je.log.entry.BINDeltaLogEntry.getResolvedItem(BINDeltaLogEntry.java:43)
        at com.sleepycat.je.tree.IN.fetchTarget(IN.java:1422)
        at com.sleepycat.je.tree.Tree.searchSubTreeInternal(Tree.java:1544)
        at com.sleepycat.je.tree.Tree.searchSubTree(Tree.java:1381)
        at com.sleepycat.je.tree.Tree.search(Tree.java:1240)
        at com.sleepycat.je.tree.Tree.getParentBINForChildLN(Tree.java:873)
        at com.sleepycat.je.cleaner.FileProcessor.processLN(FileProcessor.java:830)
        at com.sleepycat.je.cleaner.FileProcessor.processFile(FileProcessor.java:674)
        at com.sleepycat.je.cleaner.FileProcessor.doClean(FileProcessor.java:289)
        at com.sleepycat.je.cleaner.FileProcessor.onWakeup(FileProcessor.java:148)
        at com.sleepycat.je.utilint.DaemonThread.run(DaemonThread.java:163)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.FileNotFoundException: /tmp/Windup/resClfy/graph/titangraph/00000019.jdb (Too many open files)
        at java.io.RandomAccessFile.open0(Native Method)
        at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:124)
        at com.sleepycat.je.log.FileManager$DefaultRandomAccessFile.<init>(FileManager.java:3209)
        at com.sleepycat.je.log.FileManager$6.createFile(FileManager.java:3237)
        at com.sleepycat.je.log.FileManager.openFileHandle(FileManager.java:1280)
        at com.sleepycat.je.log.FileManager.getFileHandle(FileManager.java:1152)
        at com.sleepycat.je.log.LogManager.getLogSource(LogManager.java:1141)
        at com.sleepycat.je.log.LogManager.getLogEntry(LogManager.java:845)
        at com.sleepycat.je.log.LogManager.getLogEntry(LogManager.java:799)
        at com.sleepycat.je.log.LogManager.getLogEntryHandleFileNotFound(LogManager.java:860)
        ... 15 more