Neo4j: Neo4j server not starting

[noorbakerally]

I am trying to start the neo4j 3.5.7 server but failing to start on on Ubuntu 18.04. It says the the file /var/lib/neo4j/data/databases/graph.db/neostore doesn't exist while it does and with the right permission. Log is below

nohup: ignoring input
2019-08-02 22:01:47.050+0000 INFO ======== Neo4j 3.5.7 ========
2019-08-02 22:01:47.061+0000 INFO Starting...
2019-08-02 22:01:48.166+0000 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)". Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:45)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:187)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:124)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:91)
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:32)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:473)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:180)
... 3 more
Caused by: java.lang.RuntimeException: Error starting org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory, /var/lib/neo4j/data/databases
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:230)
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:146)
at org.neo4j.server.database.CommunityGraphFactory.newGraphDatabase(CommunityGraphFactory.java:41)
at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:90)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
... 5 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.NeoStoreDataSource@32c8e539' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:473)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:116)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:225)
... 9 more
Caused by: org.neo4j.kernel.impl.store.UnderlyingStorageException: java.io.FileNotFoundException: /var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)
at org.neo4j.kernel.impl.store.NeoStores.verifyRecordFormat(NeoStores.java:217)
at org.neo4j.kernel.impl.store.NeoStores.(NeoStores.java:144)
at org.neo4j.kernel.impl.store.StoreFactory.openNeoStores(StoreFactory.java:129)
at org.neo4j.kernel.impl.store.StoreFactory.openAllNeoStores(StoreFactory.java:93)
at org.neo4j.kernel.impl.storageengine.impl.recordstorage.RecordStorageEngine.(RecordStorageEngine.java:187)
at org.neo4j.kernel.NeoStoreDataSource.buildStorageEngine(NeoStoreDataSource.java:514)
at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:367)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
... 14 more
Caused by: java.io.FileNotFoundException: /var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.(RandomAccessFile.java:243)
at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:65)
at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:50)
at org.neo4j.io.pagecache.impl.SingleFilePageSwapper.(SingleFilePageSwapper.java:170)
at org.neo4j.io.pagecache.impl.SingleFilePageSwapperFactory.createPageSwapper(SingleFilePageSwapperFactory.java:66)
at org.neo4j.io.pagecache.impl.muninn.MuninnPagedFile.(MuninnPagedFile.java:149)
at org.neo4j.io.pagecache.impl.muninn.MuninnPageCache.map(MuninnPageCache.java:412)
at org.neo4j.kernel.impl.store.MetaDataStore.getRecord(MetaDataStore.java:285)
at org.neo4j.kernel.impl.store.NeoStores.verifyRecordFormat(NeoStores.java:198)
... 21 more
2019-08-02 22:01:48.167+0000 INFO Neo4j Server shutdown initiated by request
nohup: ignoring input
2019-08-02 22:03:11.329+0000 INFO ======== Neo4j 3.5.7 ========
2019-08-02 22:03:11.341+0000 INFO Starting...
2019-08-02 22:03:12.502+0000 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)". Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:45)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:187)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:124)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:91)
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:32)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:473)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:180)
... 3 more
Caused by: java.lang.RuntimeException: Error starting org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory, /var/lib/neo4j/data/databases
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:230)
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:146)
at org.neo4j.server.database.CommunityGraphFactory.newGraphDatabase(CommunityGraphFactory.java:41)
at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:90)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
... 5 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.NeoStoreDataSource@32c8e539' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:473)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:116)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:225)
... 9 more
Caused by: org.neo4j.kernel.impl.store.UnderlyingStorageException: java.io.FileNotFoundException: /var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)
at org.neo4j.kernel.impl.store.NeoStores.verifyRecordFormat(NeoStores.java:217)
at org.neo4j.kernel.impl.store.NeoStores.(NeoStores.java:144)
at org.neo4j.kernel.impl.store.StoreFactory.openNeoStores(StoreFactory.java:129)
at org.neo4j.kernel.impl.store.StoreFactory.openAllNeoStores(StoreFactory.java:93)
at org.neo4j.kernel.impl.storageengine.impl.recordstorage.RecordStorageEngine.(RecordStorageEngine.java:187)
at org.neo4j.kernel.NeoStoreDataSource.buildStorageEngine(NeoStoreDataSource.java:514)
at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:367)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
... 14 more
Caused by: java.io.FileNotFoundException: /var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.(RandomAccessFile.java:243)
at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:65)
at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:50)
at org.neo4j.io.pagecache.impl.SingleFilePageSwapper.(SingleFilePageSwapper.java:170)
at org.neo4j.io.pagecache.impl.SingleFilePageSwapperFactory.createPageSwapper(SingleFilePageSwapperFactory.java:66)
at org.neo4j.io.pagecache.impl.muninn.MuninnPagedFile.(MuninnPagedFile.java:149)
at org.neo4j.io.pagecache.impl.muninn.MuninnPageCache.map(MuninnPageCache.java:412)
at org.neo4j.kernel.impl.store.MetaDataStore.getRecord(MetaDataStore.java:285)
at org.neo4j.kernel.impl.store.NeoStores.verifyRecordFormat(NeoStores.java:198)
... 21 more
2019-08-02 22:03:12.504+0000 INFO Neo4j Server shutdown initiated by request
nohup: ignoring input
2019-08-02 22:06:18.194+0000 INFO ======== Neo4j 3.5.7 ========
2019-08-02 22:06:18.205+0000 INFO Starting...
2019-08-02 22:06:19.292+0000 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)". Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:45)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:187)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:124)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:91)
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:32)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabase@6475472c' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:473)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:180)
... 3 more
Caused by: java.lang.RuntimeException: Error starting org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory, /var/lib/neo4j/data/databases
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:230)
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:146)
at org.neo4j.server.database.CommunityGraphFactory.newGraphDatabase(CommunityGraphFactory.java:41)
at org.neo4j.server.database.LifecycleManagingDatabase.start(LifecycleManagingDatabase.java:90)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
... 5 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.NeoStoreDataSource@32c8e539' was successfully initialized, but failed to start. Please see the attached cause exception "/var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:473)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.kernel.impl.transaction.state.DataSourceManager.start(DataSourceManager.java:116)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:225)
... 9 more
Caused by: org.neo4j.kernel.impl.store.UnderlyingStorageException: java.io.FileNotFoundException: /var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)
at org.neo4j.kernel.impl.store.NeoStores.verifyRecordFormat(NeoStores.java:217)
at org.neo4j.kernel.impl.store.NeoStores.(NeoStores.java:144)
at org.neo4j.kernel.impl.store.StoreFactory.openNeoStores(StoreFactory.java:129)
at org.neo4j.kernel.impl.store.StoreFactory.openAllNeoStores(StoreFactory.java:93)
at org.neo4j.kernel.impl.storageengine.impl.recordstorage.RecordStorageEngine.(RecordStorageEngine.java:187)
at org.neo4j.kernel.NeoStoreDataSource.buildStorageEngine(NeoStoreDataSource.java:514)
at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:367)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
... 14 more
Caused by: java.io.FileNotFoundException: /var/lib/neo4j/data/databases/graph.db/neostore (Permission denied)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.(RandomAccessFile.java:243)
at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:65)
at org.neo4j.io.fs.DefaultFileSystemAbstraction.open(DefaultFileSystemAbstraction.java:50)
at org.neo4j.io.pagecache.impl.SingleFilePageSwapper.(SingleFilePageSwapper.java:170)
at org.neo4j.io.pagecache.impl.SingleFilePageSwapperFactory.createPageSwapper(SingleFilePageSwapperFactory.java:66)
at org.neo4j.io.pagecache.impl.muninn.MuninnPagedFile.(MuninnPagedFile.java:149)
at org.neo4j.io.pagecache.impl.muninn.MuninnPageCache.map(MuninnPageCache.java:412)
at org.neo4j.kernel.impl.store.MetaDataStore.getRecord(MetaDataStore.java:285)
at org.neo4j.kernel.impl.store.NeoStores.verifyRecordFormat(NeoStores.java:198)
... 21 more
2019-08-02 22:06:19.302+0000 INFO Neo4j Server shutdown initiated by request

[klaren]

The exception is FileNotFoundException but the cause of that is Permission denied.

If you could provide us with the debug.log and the output of
ls -al /var/lib/neo4j/data/databases/graph.db/
that would help to pinpoint the cause.

Thanks for reporting!

[klaren]

Closing due to inactivity. Feel free to reopen if it's still an issue.

[prashant-shahi]

I had a similar issue.

Changing the owner of graph.db folder resolved it,

chown -R neo4j.neo4j /path/to/graphdb/graph.db/