SOLVED: Jellyfin container not starting: failed to apply migrations

[themuffinman22]

Hi all,

I have Jellyfin running perfectly fine on my Unraid box for about a month with no issues. Since last week I can't access the Jellyfin library and am trying to troubleshoot. 

The container seems to be stuck in some startup issue: the webpage shows "Jellyfin is still starting, please wait" and after a few seconds crashes. RAM usage is very low (only about 60-70MB, usually in idle its 250+).

These are the container logs:

Code:

[2025-10-28 00:00:00.542 +02:00] [INF] [1] Emby.Server.Implementations.AppBase.BaseConfigurationManager: Setting cache path: "/config/cache"
[2025-10-28 00:00:01.008 +02:00] [INF] [9] Jellyfin.Server.ServerSetupApp.SetupServer: Kestrel is listening on "0.0.0.0"
[2025-10-28 00:00:01.059 +02:00] [INF] [9] Main: Jellyfin version: "10.11.0"
[2025-10-28 00:00:01.064 +02:00] [INF] [9] Main: Environment Variables: ["[JELLYFIN_LOG_DIR, /config/logs]"]
[2025-10-28 00:00:01.069 +02:00] [INF] [9] Main: Arguments: ["/usr/lib/jellyfin/jellyfin.dll", "--datadir", "/config/data", "--cachedir", "/config/cache", "--configdir", "/config/config", "--logdir", "/config/logs", "--ffmpeg", "/usr/lib/jellyfin-ffmpeg/ffmpeg", "--webdir", "/usr/share/jellyfin/web"]
[2025-10-28 00:00:01.069 +02:00] [INF] [9] Main: Operating system: "Arch Linux"
[2025-10-28 00:00:01.069 +02:00] [INF] [9] Main: Architecture: X64
[2025-10-28 00:00:01.070 +02:00] [INF] [9] Main: 64-Bit Process: True
[2025-10-28 00:00:01.070 +02:00] [INF] [9] Main: User Interactive: True
[2025-10-28 00:00:01.070 +02:00] [INF] [9] Main: Processor count: 8
[2025-10-28 00:00:01.071 +02:00] [INF] [9] Main: Program data path: "/config/data"
[2025-10-28 00:00:01.071 +02:00] [INF] [9] Main: Log directory path: "/config/logs"
[2025-10-28 00:00:01.071 +02:00] [INF] [9] Main: Config directory path: "/config/config"
[2025-10-28 00:00:01.071 +02:00] [INF] [9] Main: Cache path: "/config/cache"
[2025-10-28 00:00:01.071 +02:00] [INF] [9] Main: Temp directory path: "/tmp/jellyfin"
[2025-10-28 00:00:01.071 +02:00] [INF] [9] Main: Web resources path: "/usr/share/jellyfin/web"
[2025-10-28 00:00:01.071 +02:00] [INF] [9] Main: Application directory: "/usr/lib/jellyfin/"
[2025-10-28 00:00:01.104 +02:00] [INF] [9] Jellyfin.Server.Startup: Storage path `"/config/data/data"` (Network) successfully checked with "187.8GB" free which is over the minimum of "2GB".
[2025-10-28 00:00:01.105 +02:00] [INF] [9] Jellyfin.Server.Startup: Storage path `"/config/logs"` (Network) successfully checked with "187.8GB" free which is over the minimum of "512MB".
[2025-10-28 00:00:01.106 +02:00] [INF] [9] Jellyfin.Server.Startup: Storage path `"/config/cache"` (Network) successfully checked with "187.8GB" free which is over the minimum of "2GB".
[2025-10-28 00:00:01.107 +02:00] [INF] [9] Jellyfin.Server.Startup: Storage path `"/config/data"` (Network) successfully checked with "187.8GB" free which is over the minimum of "2GB".
[2025-10-28 00:00:01.107 +02:00] [INF] [9] Jellyfin.Server.Startup: Storage path `"/tmp/jellyfin"` (Fixed) successfully checked with "5GB" free which is over the minimum of "2GB".
[2025-10-28 00:00:01.113 +02:00] [INF] [9] Emby.Server.Implementations.AppBase.BaseConfigurationManager: Setting cache path: "/config/cache"
[2025-10-28 00:00:01.245 +02:00] [INF] [9] Jellyfin.Database.Providers.Sqlite.SqliteDatabaseProvider: SQLite connection string: "Data Source=/config/data/data/jellyfin.db;Cache=Default;Pooling=True"
[2025-10-28 00:00:01.259 +02:00] [INF] [9] Jellyfin.Database.Providers.Sqlite.SqliteDatabaseProvider: SQLITE connection pragma command set to:
"PRAGMA locking_mode=NORMAL;
PRAGMA journal_size_limit=134217728;
PRAGMA synchronous=1;
PRAGMA temp_store=2;
"
[2025-10-28 00:00:01.261 +02:00] [INF] [9] Jellyfin.Database.Implementations.Locking.NoLockBehavior: The database locking mode has been set to: NoLock.
[2025-10-28 00:00:01.314 +02:00] [INF] [9] Jellyfin.Server.Migrations.JellyfinMigrationService: Initialise Migration service.
[2025-10-28 00:00:01.329 +02:00] [INF] [9] Jellyfin.Server.Migrations.JellyfinMigrationService: Old migration style migration.xml detected. Migrate now.
[2025-10-28 00:00:03.685 +02:00] [FTL] [9] Jellyfin.Server.Migrations.JellyfinMigrationService: Failed to apply migrations
System.InvalidOperationException: Sequence contains no elements
  at System.Linq.ThrowHelper.ThrowNoElementsException()
  at System.Linq.Enumerable.Last[TSource](IEnumerable`1 source)
  at Jellyfin.Server.Migrations.JellyfinMigrationService.CheckFirstTimeRunOrMigration(IApplicationPaths appPaths)
  at Jellyfin.Server.Migrations.JellyfinMigrationService.CheckFirstTimeRunOrMigration(IApplicationPaths appPaths)
[2025-10-28 00:00:03.699 +02:00] [FTL] [1] Main: Unhandled Exception
System.InvalidOperationException: Sequence contains no elements
  at System.Linq.ThrowHelper.ThrowNoElementsException()
  at System.Linq.Enumerable.Last[TSource](IEnumerable`1 source)
  at Jellyfin.Server.Migrations.JellyfinMigrationService.CheckFirstTimeRunOrMigration(IApplicationPaths appPaths)
  at Jellyfin.Server.Migrations.JellyfinMigrationService.CheckFirstTimeRunOrMigration(IApplicationPaths appPaths)
  at Jellyfin.Server.Program.ApplyStartupMigrationAsync(ServerApplicationPaths appPaths, IConfiguration startupConfig)
  at Jellyfin.Server.Program.StartApp(StartupOptions options)
  at Jellyfin.Server.Program.<Main>(String[] args)

This keeps repeating as the container tries to start.
I have no idea how to fix this, I'd like not to lose the library I have so if possible I'd like not to reinstall the container (unless I can keep the library somehow). Thanks a lot in advance

[themuffinman22]

Ok just removing and repulling the container (without deleting the image) worked...