Upgrade from 3.1.0-04 to 3.12.1-01 failed with error in database


#1

Hello everybody,

I tried to Upgrade our nexus from version 3.1.0-04 to 3.12.1-01. Its failed everytime with the following error, the main Quesion is, why he have issues to write to the accesslog/*? The Permissions are right for the user and he owns both directorys. If you need additional information, let me know.

...
2018-07-02 16:50:15,854+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseServerImpl - Activated
2018-07-02 16:50:15,965+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.extender.NexusLifecycleManager - Start RESTORE
2018-07-02 16:50:16,315+0000 INFO  [ForkJoinPool.commonPool-worker-1]  *SYSTEM ROOT - Storage 'plocal:/opt/sonatype-work/nexus3/db/analytics' is opened under OrientDB distribution : 2.2.34 (build f340442755a31eabc91b87cb3ef99eda5cee6ebd, branch 2.2.x)
2018-07-02 16:50:16,327+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - Storage 'plocal:/opt/sonatype-work/nexus3/db/config' is opened under OrientDB distribution : 2.2.34 (build f340442755a31eabc91b87cb3ef99eda5cee6ebd, branch 2.2.x)
2018-07-02 16:50:16,905+0000 INFO  [ForkJoinPool.commonPool-worker-1]  *SYSTEM ROOT - Storage 'plocal:/opt/sonatype-work/nexus3/db/audit' is opened under OrientDB distribution : 2.2.34 (build f340442755a31eabc91b87cb3ef99eda5cee6ebd, branch 2.2.x)
2018-07-02 16:50:16,923+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - Storage 'plocal:/opt/sonatype-work/nexus3/db/security' is opened under OrientDB distribution : 2.2.34 (build f340442755a31eabc91b87cb3ef99eda5cee6ebd, branch 2.2.x)
2018-07-02 16:50:17,056+0000 WARN  [ForkJoinPool.commonPool-worker-1]  *SYSTEM ROOT - Main storage configuration file /opt/sonatype-work/nexus3/db/accesslog/database.ocf is broken in storage accesslog, try to read from backup file /opt/sonatype-work/nexus3/db/accesslog/database.ocf2
2018-07-02 16:50:17,057+0000 ERROR [ForkJoinPool.commonPool-worker-1]  *SYSTEM ROOT - Backup configuration file /opt/sonatype-work/nexus3/db/accesslog/database.ocf2 does not exist
2018-07-02 16:50:17,084+0000 ERROR [ForkJoinPool.commonPool-worker-1]  *SYSTEM ROOT - Exception `667C2A59` in storage `plocal:/opt/sonatype-work/nexus3/db/accesslog`: 2.2.34 (build f340442755a31eabc91b87cb3ef99eda5cee6ebd, branch 2.2.x)
com.orientechnologies.orient.core.exception.OStorageException: Cannot open local storage '/opt/sonatype-work/nexus3/db/accesslog' with mode=rw
	DB name="accesslog"
	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:323)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.open(ODatabaseDocumentTx.java:259)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.connect(DatabaseManagerSupport.java:143)
	at org.sonatype.nexus.orient.DatabaseInstanceImpl.doStart(DatabaseInstanceImpl.java:56)
	at org.sonatype.goodies.lifecycle.LifecycleSupport.start(LifecycleSupport.java:104)
	at org.sonatype.goodies.lifecycle.Lifecycles.start(Lifecycles.java:44)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.createInstance(DatabaseManagerSupport.java:252)
	at java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1660)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.instance(DatabaseManagerSupport.java:231)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
	at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:291)
	at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.execLocalTasks(ForkJoinPool.java:1040)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1058)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
Caused by: com.orientechnologies.orient.core.exception.OStorageException: Invalid format for configuration file /opt/sonatype-work/nexus3/db/accesslog/database.ocf for storageaccesslog
	DB name="accesslog"
	at com.orientechnologies.orient.core.storage.impl.local.OStorageConfigurationSegment.load(OStorageConfigurationSegment.java:152)
	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:267)
	... 18 common frames omitted
2018-07-02 16:50:17,085+0000 ERROR [ForkJoinPool.commonPool-worker-1]  *SYSTEM org.sonatype.nexus.orient.DatabaseInstanceImpl - Lifecycle operation start failed
com.orientechnologies.orient.core.exception.OStorageException: Cannot open local storage '/opt/sonatype-work/nexus3/db/accesslog' with mode=rw
	DB name="accesslog"
	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:323)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.open(ODatabaseDocumentTx.java:259)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.connect(DatabaseManagerSupport.java:143)
	at org.sonatype.nexus.orient.DatabaseInstanceImpl.doStart(DatabaseInstanceImpl.java:56)
	at org.sonatype.goodies.lifecycle.LifecycleSupport.start(LifecycleSupport.java:104)
	at org.sonatype.goodies.lifecycle.Lifecycles.start(Lifecycles.java:44)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.createInstance(DatabaseManagerSupport.java:252)
	at java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1660)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.instance(DatabaseManagerSupport.java:231)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
	at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:291)
	at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.execLocalTasks(ForkJoinPool.java:1040)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1058)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
Caused by: com.orientechnologies.orient.core.exception.OStorageException: Invalid format for configuration file /opt/sonatype-work/nexus3/db/accesslog/database.ocf for storageaccesslog
	DB name="accesslog"
	at com.orientechnologies.orient.core.storage.impl.local.OStorageConfigurationSegment.load(OStorageConfigurationSegment.java:152)
	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:267)
	... 18 common frames omitted
2018-07-02 16:50:17,132+0000 ERROR [FelixStartLevel]  *SYSTEM org.sonatype.nexus.orient.restore.RestoreServiceImpl - Failed transition: NEW -> STARTED
com.orientechnologies.orient.core.exception.OStorageException: Cannot open local storage '/opt/sonatype-work/nexus3/db/accesslog' with mode=rw
	DB name="accesslog"
	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:323)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.open(ODatabaseDocumentTx.java:259)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.connect(DatabaseManagerSupport.java:143)
	at org.sonatype.nexus.orient.DatabaseInstanceImpl.doStart(DatabaseInstanceImpl.java:56)
	at org.sonatype.goodies.lifecycle.LifecycleSupport.start(LifecycleSupport.java:104)
	at org.sonatype.goodies.lifecycle.Lifecycles.start(Lifecycles.java:44)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.createInstance(DatabaseManagerSupport.java:252)
	at java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1660)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.instance(DatabaseManagerSupport.java:231)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
	at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:291)
	at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.execLocalTasks(ForkJoinPool.java:1040)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1058)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
Caused by: com.orientechnologies.orient.core.exception.OStorageException: Invalid format for configuration file /opt/sonatype-work/nexus3/db/accesslog/database.ocf for storageaccesslog
	DB name="accesslog"
	at com.orientechnologies.orient.core.storage.impl.local.OStorageConfigurationSegment.load(OStorageConfigurationSegment.java:152)
	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:267)
	... 18 common frames omitted
2018-07-02 16:50:17,132+0000 ERROR [FelixStartLevel]  *SYSTEM org.sonatype.nexus.extender.NexusContextListener - Failed to start nexus
com.orientechnologies.orient.core.exception.OStorageException: Cannot open local storage '/opt/sonatype-work/nexus3/db/accesslog' with mode=rw
	DB name="accesslog"
	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:323)
	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.open(ODatabaseDocumentTx.java:259)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.connect(DatabaseManagerSupport.java:143)
	at org.sonatype.nexus.orient.DatabaseInstanceImpl.doStart(DatabaseInstanceImpl.java:56)
	at org.sonatype.goodies.lifecycle.LifecycleSupport.start(LifecycleSupport.java:104)
	at org.sonatype.goodies.lifecycle.Lifecycles.start(Lifecycles.java:44)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.createInstance(DatabaseManagerSupport.java:252)
	at java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1660)
	at org.sonatype.nexus.orient.DatabaseManagerSupport.instance(DatabaseManagerSupport.java:231)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
	at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:291)
	at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
	at java.util.concurrent.ForkJoinPool$WorkQueue.execLocalTasks(ForkJoinPool.java:1040)
	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1058)
	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
Caused by: com.orientechnologies.orient.core.exception.OStorageException: Invalid format for configuration file /opt/sonatype-work/nexus3/db/accesslog/database.ocf for storageaccesslog
	DB name="accesslog"
	at com.orientechnologies.orient.core.storage.impl.local.OStorageConfigurationSegment.load(OStorageConfigurationSegment.java:152)
	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:267)
	... 18 common frames omitted
2018-07-02 16:50:17,134+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - com.orientechnologies.orient.core.exception.OStorageException: Cannot open local storage '/opt/sonatype-work/nexus3/db/accesslog' with mode=rw
	DB name="accesslog"
2018-07-02 16:50:17,134+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:323)
2018-07-02 16:50:17,134+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.open(ODatabaseDocumentTx.java:259)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at org.sonatype.nexus.orient.DatabaseManagerSupport.connect(DatabaseManagerSupport.java:143)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at org.sonatype.nexus.orient.DatabaseInstanceImpl.doStart(DatabaseInstanceImpl.java:56)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at org.sonatype.goodies.lifecycle.LifecycleSupport.start(LifecycleSupport.java:104)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at org.sonatype.goodies.lifecycle.Lifecycles.start(Lifecycles.java:44)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at org.sonatype.nexus.orient.DatabaseManagerSupport.createInstance(DatabaseManagerSupport.java:252)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1660)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at org.sonatype.nexus.orient.DatabaseManagerSupport.instance(DatabaseManagerSupport.java:231)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
2018-07-02 16:50:17,135+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:291)
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.concurrent.ForkJoinPool$WorkQueue.execLocalTasks(ForkJoinPool.java:1040)
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1058)
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - Caused by: com.orientechnologies.orient.core.exception.OStorageException: Invalid format for configuration file /opt/sonatype-work/nexus3/db/accesslog/database.ocf for storageaccesslog
	DB name="accesslog"
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at com.orientechnologies.orient.core.storage.impl.local.OStorageConfigurationSegment.load(OStorageConfigurationSegment.java:152)
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:267)
2018-07-02 16:50:17,136+0000 ERROR [FelixStartLevel]  *SYSTEM java.lang.Throwable - 	... 18 more
2018-07-02 16:50:17,559+0000 INFO  [ForkJoinPool.commonPool-worker-1]  *SYSTEM ROOT - Storage 'plocal:/opt/sonatype-work/nexus3/db/component' is opened under OrientDB distribution : 2.2.34 (build f340442755a31eabc91b87cb3ef99eda5cee6ebd, branch 2.2.x)
2018-07-02 16:50:17,563+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.extender.NexusContextListener - Uptime: 16 seconds and 68 milliseconds
2018-07-02 16:50:17,566+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.extender.NexusLifecycleManager - Stop STORAGE
2018-07-02 16:50:17,567+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping 6 pools
2018-07-02 16:50:17,567+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping pool: analytics
2018-07-02 16:50:17,567+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping pool: security
2018-07-02 16:50:17,567+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping pool: component
2018-07-02 16:50:17,567+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping pool: audit
2018-07-02 16:50:17,568+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping pool: config
2018-07-02 16:50:17,568+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping pool: accesslog
2018-07-02 16:50:17,568+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping 4 instances
2018-07-02 16:50:17,568+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping instance: analytics
2018-07-02 16:50:17,568+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping instance: security
2018-07-02 16:50:17,708+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping instance: audit
2018-07-02 16:50:17,708+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseManagerImpl - Stopping instance: config
2018-07-02 16:50:17,708+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - OrientDB Server is shutting down...
2018-07-02 16:50:17,708+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - Shutting down protocols
2018-07-02 16:50:17,709+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - Shutting down plugins:
2018-07-02 16:50:17,709+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - - jmx
2018-07-02 16:50:17,709+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - Shutting down databases:
2018-07-02 16:50:17,709+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - Orient Engine is shutting down...
2018-07-02 16:50:17,710+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - - shutdown storage: analytics...
2018-07-02 16:50:17,740+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - - shutdown storage: security...
2018-07-02 16:50:17,767+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - - shutdown storage: component...
2018-07-02 16:50:17,790+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - - shutdown storage: audit...
2018-07-02 16:50:17,803+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - - shutdown storage: config...
2018-07-02 16:50:17,830+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - - shutdown storage: OSystem...
2018-07-02 16:50:17,832+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - - shutdown storage: accesslog...
2018-07-02 16:50:18,208+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - OrientDB Engine shutdown complete
2018-07-02 16:50:18,212+0000 INFO  [FelixStartLevel]  *SYSTEM ROOT - OrientDB Server shutdown complete
2018-07-02 16:50:18,214+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.internal.orient.DatabaseServerImpl - Shutdown
2018-07-02 16:50:18,215+0000 INFO  [FelixStartLevel]  *SYSTEM org.sonatype.nexus.extender.NexusLifecycleManager - Stop KERNEL

#2

Caused by: com.orientechnologies.orient.core.exception.OStorageException: Invalid format for configuration file /opt/sonatype-work/nexus3/db/accesslog/database.ocf for storageaccesslog

Looks like something is wrong with the access log database. That database just keeps track of IP addresses that have contacted Nexus, it’s not essential.

Can you try renaming " /opt/sonatype-work/nexus3/db/accesslog" to " /opt/sonatype-work/nexus3/db/accesslog.old"?