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getting error database disk image is malformed. - Printable Version

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getting error database disk image is malformed. - justtrife - 2025-08-19

installed linux mint fresh along w/ a fresh copy of jellyfin (about a week old install at this point)

initially installed jellyfin via the software manager but i had some issues w/ the flatpak version so i uninstalled it via the software manager and feeling like that wasn't enough, i purged it using 

Code:
sudo apt purge jellyfin*

and then ran 

Code:
sudo rm -rf /var/lib/jellyfin /etc/jellyfin /var/cache/jellyfin /usr/share/jellyfin

i then re-installed jellyfin using 

Code:
curl https://repo.jellyfin.org/install-debuntu.sh | sudo bash

made sure to enable it at boot w/

Code:
sudo systemctl enable jellyfin

after configuring it, i noticed that one of the libraries disappeared from the recently added media list on the home page, I originally planned to look into it further but... life.

about 3hrs after i noticed the missing library i rebooted the entire system after installing jellyfin plugins and updating already installed apps on the system.

jellyfin now refuses to start after reboot, so i ran this

Code:
justtrife@Pandoras-Box:~$ sudo systemctl status jellyfin
○ jellyfin.service - Jellyfin Media Server
    Loaded: loaded (/usr/lib/systemd/system/jellyfin.service; enabled; preset: enabled)
    Drop-In: /etc/systemd/system/jellyfin.service.d
            └─jellyfin.service.conf
    Active: inactive (dead) since Mon 2025-08-18 21:53:07 CDT; 6min ago
  Duration: 1.223s
    Process: 76182 ExecStart=/usr/bin/jellyfin $JELLYFIN_WEB_OPT $JELLYFIN_FFMPEG_OPT $JELLYFIN_SERVICE_OPT $JELLYFIN_NOWEBAPP_OPT $JELLYFIN_ADDITIONAL_OPTS (code=exited, status=0/SUCCESS)
  Main PID: 76182 (code=exited, status=0/SUCCESS)
        CPU: 1.236s

Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Emby.Server.Implementations.Data.ManagedConnection.Execute(String commandText)
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Emby.Server.Implementations.Data.BaseSqliteRepository.Initialize()
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Emby.Server.Implementations.Data.SqliteItemRepository.Initialize()
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Emby.Server.Implementations.ApplicationHost.InitializeServices()
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Jellyfin.Server.Program.StartServer(IServerApplicationPaths appPaths, StartupOptions options, IConfiguration startupConfig)
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]: [21:53:07] [INF] Running query planner optimizations in the database... This might take a while
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]: [21:53:07] [INF] Disposing CoreAppHost
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]: [21:53:07] [INF] Disposing PluginManager
Aug 18 21:53:07 Pandoras-Box systemd[1]: jellyfin.service: Deactivated successfully.
Aug 18 21:53:07 Pandoras-Box systemd[1]: jellyfin.service: Consumed 1.236s CPU time.

initially thought that was odd so i started it again with the command 

Code:
sudo systemctl start jellyfin

and then checked the status immediately after and got the EXACT same thing as above.

in effort to figure out what exactly was causing this i ran 

Code:
sudo journalctl -u jellyfin
 

and i got this

Code:
Aug 18 21:53:06 Pandoras-Box systemd[1]: Started jellyfin.service - Jellyfin Media Server.
Aug 18 21:53:06 Pandoras-Box (jellyfin)[76182]: jellyfin.service: Referenced but unset environment variable evaluates to an empty string: JELLYFIN_NOWEBAPP_OPT, JELLYFIN_SERVICE_OPT
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Jellyfin version: 10.10.7
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Environment Variables: ["[JELLYFIN_FFMPEG_OPT, --ffmpeg=/usr/lib/jellyfin-ffmpeg/ffmpeg]", "[JELLYFIN_CACHE_DIR, /var/cache/jellyfin]", "[JELLYFIN_DATA_DIR, /var/lib/jellyfin]", "[JELLYFIN_ARGS, $JELLYFIN_WEB_OPT $JELLYFIN_FFMPEG_OPT $JELLYFIN_SERVICE_OPT $JELLYFIN_NOWEBAPP_OPT $JELLFIN_ADDITIONAL_OPTS --datadir $JELLYFIN_DATA_DIR --configdir $JELLYFIN_CONFIG_DI>
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Arguments: ["/usr/lib/jellyfin/bin/jellyfin.dll", "--webdir=/usr/share/jellyfin/web", "--ffmpeg=/usr/lib/jellyfin-ffmpeg/ffmpeg"]
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Operating system: Linux Mint 22.1
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Architecture: X64
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] 64-Bit Process: True
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] User Interactive: True
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Processor count: 16
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Program data path: /var/lib/jellyfin
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Log directory path: /var/log/jellyfin
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Config directory path: /etc/jellyfin
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Cache path: /var/cache/jellyfin
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Temp directory path: /tmp/jellyfin
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Web resources path: /usr/share/jellyfin/web
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Application directory: /usr/lib/jellyfin/bin/
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Marking following migrations as applied because this is a fresh install: ["CreateNetworkConfiguration", "MigrateMusicBrainzTimeout", "MigrateNetworkConfiguration", "MigrateEncodingOptions"]
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Setting cache path: /var/cache/jellyfin
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loading assemblies
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.AniDB, Version=10.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/AniDB_10.0.0.0/Jellyfin.Plugin.AniDB.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.AniList, Version=11.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/AniList_11.0.0.0/Jellyfin.Plugin.AniList.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.AniSearch, Version=5.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/AniSearch_5.0.0.0/Jellyfin.Plugin.AniSearch.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Artwork, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Artwork_1.0.0.0/Jellyfin.Plugin.Artwork.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Bookshelf, Version=12.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Bookshelf_12.0.0.0/Jellyfin.Plugin.Bookshelf.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly ZstdSharp, Version=0.8.1.0, Culture=neutral, PublicKeyToken=8d151af33a4ad5cf from /var/lib/jellyfin/plugins/Bookshelf_12.0.0.0/ZstdSharp.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly SharpCompress, Version=0.38.0.0, Culture=neutral, PublicKeyToken=afb0a02973931d96 from /var/lib/jellyfin/plugins/Bookshelf_12.0.0.0/SharpCompress.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Dlna, Version=8.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/DLNA_8.0.0.0/Jellyfin.Plugin.Dlna.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Dlna.Playback, Version=8.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/DLNA_8.0.0.0/Jellyfin.Plugin.Dlna.Playback.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Rssdp, Version=8.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/DLNA_8.0.0.0/Rssdp.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Dlna.Model, Version=8.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/DLNA_8.0.0.0/Jellyfin.Plugin.Dlna.Model.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Fanart, Version=12.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Fanart_12.0.0.0/Jellyfin.Plugin.Fanart.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.IMVDb, Version=4.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/IMVDb_4.0.0.0/Jellyfin.Plugin.IMVDb.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Kitsu, Version=6.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Kitsu_6.0.0.0/Jellyfin.Plugin.Kitsu.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Opds, Version=6.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/OPDS_6.0.0.0/Jellyfin.Plugin.Opds.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.OpenSubtitles, Version=20.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Open Subtitles_20.0.0.0/Jellyfin.Plugin.OpenSubtitles.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly SQLitePCL.pretty, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Playback Reporting_16.0.0.0/SQLitePCL.pretty.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.PlaybackReporting, Version=16.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Playback Reporting_16.0.0.0/Jellyfin.Plugin.PlaybackReporting.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly ClosedXML, Version=0.97.0.0, Culture=neutral, PublicKeyToken=fd1eb21b62ae805b from /var/lib/jellyfin/plugins/Reports_17.0.0.0/ClosedXML.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly SixLabors.Fonts, Version=1.0.0.0, Culture=neutral, PublicKeyToken=d998eea7b14cab13 from /var/lib/jellyfin/plugins/Reports_17.0.0.0/SixLabors.Fonts.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly ExcelNumberFormat, Version=1.1.0.0, Culture=neutral, PublicKeyToken=23c6f5d73be07eca from /var/lib/jellyfin/plugins/Reports_17.0.0.0/ExcelNumberFormat.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly DocumentFormat.OpenXml, Version=2.16.0.0, Culture=neutral, PublicKeyToken=8fb06cb64d019a17 from /var/lib/jellyfin/plugins/Reports_17.0.0.0/DocumentFormat.OpenXml.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly System.IO.Packaging, Version=4.0.5.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a from /var/lib/jellyfin/plugins/Reports_17.0.0.0/System.IO.Packaging.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Reports, Version=17.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Reports_17.0.0.0/Jellyfin.Plugin.Reports.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.SessionCleaner, Version=4.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Session Cleaner_4.0.0.0/Jellyfin.Plugin.SessionCleaner.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.SubtitleExtract, Version=4.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/Subtitle Extract_4.0.0.0/Jellyfin.Plugin.SubtitleExtract.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.Tvdb, Version=19.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/TheTVDB_19.0.0.0/Jellyfin.Plugin.Tvdb.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Tvdb.Sdk, Version=4.7.10.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/TheTVDB_19.0.0.0/Tvdb.Sdk.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.TMDbBoxSets, Version=11.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/TMDb Box Sets_11.0.0.0/Jellyfin.Plugin.TMDbBoxSets.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly TvMaze.Api.Client, Version=0.1.72.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/TVmaze_12.0.0.0/TvMaze.Api.Client.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Flurl, Version=3.0.1.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/TVmaze_12.0.0.0/Flurl.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Polly, Version=7.0.0.0, Culture=neutral, PublicKeyToken=c8a3ffc3f8f825cc from /var/lib/jellyfin/plugins/TVmaze_12.0.0.0/Polly.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Flurl.Http, Version=3.0.1.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/TVmaze_12.0.0.0/Flurl.Http.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Loaded assembly Jellyfin.Plugin.TvMaze, Version=12.0.0.0, Culture=neutral, PublicKeyToken=null from /var/lib/jellyfin/plugins/TVmaze_12.0.0.0/Jellyfin.Plugin.TvMaze.dll
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Defined LAN subnets: ["127.0.0.1/8", "10.0.0.0/8", "172.16.0.0/12", "192.168.0.0/16"]
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Defined LAN exclusions: []
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Used LAN subnets: ["127.0.0.1/8", "10.0.0.0/8", "172.16.0.0/12", "192.168.0.0/16"]
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Filtered interface addresses: ["127.0.0.1", "192.168.1.99"]
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Bind Addresses ["0.0.0.0"]
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Remote IP filter is Allowlist
Aug 18 21:53:06 Pandoras-Box jellyfin[76182]: [21:53:06] [INF] Filtered subnets: []
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]: [21:53:07] [FTL] Error while starting server
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]: Microsoft.Data.Sqlite.SqliteException (0x80004005): SQLite Error 11: 'database disk image is malformed'.
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Microsoft.Data.Sqlite.SqliteException.ThrowExceptionForRC(Int32 rc, sqlite3 db)
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Microsoft.Data.Sqlite.SqliteDataReader.NextResult()
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Microsoft.Data.Sqlite.SqliteCommand.ExecuteReader(CommandBehavior behavior)
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Microsoft.Data.Sqlite.SqliteCommand.ExecuteReader()
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Microsoft.Data.Sqlite.SqliteCommand.ExecuteNonQuery()
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Emby.Server.Implementations.Data.SqliteExtensions.Execute(SqliteConnection sqliteConnection, String commandText)
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Emby.Server.Implementations.Data.ManagedConnection.Execute(String commandText)
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Emby.Server.Implementations.Data.BaseSqliteRepository.Initialize()
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Emby.Server.Implementations.Data.SqliteItemRepository.Initialize()
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Emby.Server.Implementations.ApplicationHost.InitializeServices()
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]:    at Jellyfin.Server.Program.StartServer(IServerApplicationPaths appPaths, StartupOptions options, IConfiguration startupConfig)
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]: [21:53:07] [INF] Running query planner optimizations in the database... This might take a while
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]: [21:53:07] [INF] Disposing CoreAppHost
Aug 18 21:53:07 Pandoras-Box jellyfin[76182]: [21:53:07] [INF] Disposing PluginManager
Aug 18 21:53:07 Pandoras-Box systemd[1]: jellyfin.service: Deactivated successfully.
Aug 18 21:53:07 Pandoras-Box systemd[1]: jellyfin.service: Consumed 1.236s CPU time.

i am now at a loss as of this moment on how to move foward. any help would be greatly appreciated.

i am comfortable w/ linux but have a lot to learn in the way of terminal commands but am eager to learn so that way i can triage these situations on my own in the future, if you could accompany any advice along w/ the commands needed to complete them, it would be greatly appreciated.