I am seeing an error (below) when using some of the downstream functions in Pantools, such as add_annotations and map. I am not familiar with neo4j, but it seems to occur when the pangenome database is started. These pangenome builds have not previously caused a problem, but once this error is reported - I am unable to access the database any more. I think it is happening if a Pantools task is interrupted, and neo4j doesn't exit the database correctly - leaving it corrupted and unable to be started for the next task.
Is there a way I can avoid this?
Many thanks
Rachel
Mapping single or paired-end short reads to the pangenome
No number of threads are selected via --threads or -tn, using 1
No --max-fragment-length was set. Default is 5000
Starting the pangenome databaseException in thread "main" java.lang.RuntimeException: Error starting org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory, /ei/projects/9/90a2cc84-e6dd-40a3-ab23-38dcd2389ff0/data/pangenome/pangenome_33_neo4j_corrupted/databases
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:216)
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:135)
at org.neo4j.graphdb.factory.GraphDatabaseFactory.newDatabase(GraphDatabaseFactory.java:133)
at org.neo4j.graphdb.factory.GraphDatabaseFactory.newEmbeddedDatabase(GraphDatabaseFactory.java:122)
at org.neo4j.graphdb.factory.GraphDatabaseFactory$EmbeddedDatabaseCreator.newDatabase(GraphDatabaseFactory.java:178)
at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:210)
at pantools.Pantools.connect_pangenome(Pantools.java:1123)
at pangenome.GenomeLayer.map_reads(GenomeLayer.java:1851)
at pantools.Pantools.main(Pantools.java:1036)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.NeoStoreDataSource@7fcff1b9' was successfully initialized, but failed to start. Please see the attached cause exception "No check point found in any log file from version 332 to 332".
at org.neo4j.kernel.lifecycle.LifeSupport$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$LifecycleInstance.start(LifeSupport.java:452)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:211)
... 8 more
Caused by: java.lang.RuntimeException: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.recovery.Recovery@288a4658' failed to initialize. Please see the attached cause exception "No check point found in any log file from version 332 to 332".
at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:450)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452)
... 13 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.recovery.Recovery@288a4658' failed to initialize. Please see the attached cause exception "No check point found in any log file from version 332 to 332".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:434)
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:66)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:102)
at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:434)
... 14 more
Caused by: org.neo4j.kernel.impl.store.UnderlyingStorageException: No check point found in any log file from version 332 to 332
at org.neo4j.kernel.recovery.RecoveryStartInformationProvider.get(RecoveryStartInformationProvider.java:108)
at org.neo4j.kernel.recovery.DefaultRecoveryService.getRecoveryStartInformation(DefaultRecoveryService.java:61)
at org.neo4j.kernel.recovery.Recovery.init(Recovery.java:64)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:413)
... 17 more
Hi there,
I am seeing an error (below) when using some of the downstream functions in Pantools, such as add_annotations and map. I am not familiar with neo4j, but it seems to occur when the pangenome database is started. These pangenome builds have not previously caused a problem, but once this error is reported - I am unable to access the database any more. I think it is happening if a Pantools task is interrupted, and neo4j doesn't exit the database correctly - leaving it corrupted and unable to be started for the next task.
Is there a way I can avoid this? Many thanks Rachel
------------------------------- PanTools 3.2 ------------------------------ WORKING_DIRECTORY = pangenome_33_neo4j_corrupted/ PATH_TO_THE_FIRST_SRA = test_datasets/sim_reads_R1.fq.gz PATH_TO_THE_SECOND_SRA = test_datasets/sim_reads_R2.fq.gz PATH_TO_THE_GENOME_NUMBERS_FILE = genome_numbers.txt MIN_IDENTITY = 0.5 NUM_KMER_SAMPLES = 15 MAX_NUM_LOCATIONS = 15 ALIGNMENT_BOUND = 5 CLIPPING_STRINGENCY = 1
Mapping single or paired-end short reads to the pangenome
No number of threads are selected via --threads or -tn, using 1 No --max-fragment-length was set. Default is 5000 Starting the pangenome databaseException in thread "main" java.lang.RuntimeException: Error starting org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory, /ei/projects/9/90a2cc84-e6dd-40a3-ab23-38dcd2389ff0/data/pangenome/pangenome_33_neo4j_corrupted/databases at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:216) at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.newFacade(GraphDatabaseFacadeFactory.java:135) at org.neo4j.graphdb.factory.GraphDatabaseFactory.newDatabase(GraphDatabaseFactory.java:133) at org.neo4j.graphdb.factory.GraphDatabaseFactory.newEmbeddedDatabase(GraphDatabaseFactory.java:122) at org.neo4j.graphdb.factory.GraphDatabaseFactory$EmbeddedDatabaseCreator.newDatabase(GraphDatabaseFactory.java:178) at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:210) at pantools.Pantools.connect_pangenome(Pantools.java:1123) at pangenome.GenomeLayer.map_reads(GenomeLayer.java:1851) at pantools.Pantools.main(Pantools.java:1036) Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.NeoStoreDataSource@7fcff1b9' was successfully initialized, but failed to start. Please see the attached cause exception "No check point found in any log file from version 332 to 332". at org.neo4j.kernel.lifecycle.LifeSupport$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$LifecycleInstance.start(LifeSupport.java:452) at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111) at org.neo4j.graphdb.facade.GraphDatabaseFacadeFactory.initFacade(GraphDatabaseFacadeFactory.java:211) ... 8 more Caused by: java.lang.RuntimeException: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.recovery.Recovery@288a4658' failed to initialize. Please see the attached cause exception "No check point found in any log file from version 332 to 332". at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:450) at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:452) ... 13 more Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.recovery.Recovery@288a4658' failed to initialize. Please see the attached cause exception "No check point found in any log file from version 332 to 332". at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:434) at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:66) at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:102) at org.neo4j.kernel.NeoStoreDataSource.start(NeoStoreDataSource.java:434) ... 14 more Caused by: org.neo4j.kernel.impl.store.UnderlyingStorageException: No check point found in any log file from version 332 to 332 at org.neo4j.kernel.recovery.RecoveryStartInformationProvider.get(RecoveryStartInformationProvider.java:108) at org.neo4j.kernel.recovery.DefaultRecoveryService.getRecoveryStartInformation(DefaultRecoveryService.java:61) at org.neo4j.kernel.recovery.Recovery.init(Recovery.java:64) at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:413) ... 17 more