SqliteError: database disk image is malformed

[doobes]

What do I do about this?

15:12:42.074 SqliteError: database disk image is malformed
15:12:45.961 Table counts: notes: 2000, revisions: 651, attachments: 1639, branches: 2017, attributes: 2278, etapi_tokens: 0, blobs: 29
15:12:46.004 SqliteError: database disk image is malformed
15:13:01.767 304 GET /api/setup/status with 59 bytes took 8ms
15:13:01.800 Slow 200 POST /api/login/sync with 55 bytes took 12ms
15:13:01.809 Sending message to all clients: {"type":"sync-pull-in-progress","lastSyncedPush":0}
15:13:01.813 ERROR: put /api/sync/update threw exception: 'database disk image is malformed', stack: SqliteError: database disk image i
at /usr/src/app/main.cjs:963:246
at Q5 (/usr/src/app/main.cjs:963:1591)
at Object.A6i [as getRow] (/usr/src/app/main.cjs:963:236)
at DGi (/usr/src/app/main.cjs:1606:59685)
at RGi (/usr/src/app/main.cjs:1606:59462)
at Object.NGi [as updateEntities] (/usr/src/app/main.cjs:1606:59336)
at sqliteTransaction. (/usr/src/app/main.cjs:1860:577)
at sqliteTransaction (/usr/src/app/node_modules/better-sqlite3/lib/methods/transaction.js:65:24)
at Object.C6i [as transactional] (/usr/src/app/main.cjs:963:1970)
at $Wi (/usr/src/app/main.cjs:1860:555)

The database integrity check gives a long list of issues that I can't see the end of. Clicking the "Find and Fix Consistency Issues" says it works, but the integrity check still gives a long list of issues.

Thank you

[eliandoran]

What was the installation method and does it occur on the desktop or the client?

Did you, by any chance, share the database over NFS or SMB? If so, that's what caused the database to be corrupted.

Either way, the database is corrupted so the solution is to restore from a backup or if this is the desktop client that got corrupted, to remove the database and do a fresh sync with the server.

[doobes]

Ok. I copied a backup db to the storage location.

Everything works fine in a Windows version of Trilium.

I updated my Pop!_OS Cosmic flatpak, removed all the config info (in .config, and .share) and started up a new Trilium instance.

This is what I'm getting:

As you can see, the Trilium browser version is running in the background.

My head hurts

[eliandoran]

@doobes , try removing the /at the end of the address.

[doobes]

Looking in my logs, the application is continually terminating and restarting.

How do I figure out why?

[eliandoran]

Can you post the logs?

[doobes]

2025-12-12T17:35:45.630561032Z CSRF token generation: Successful
2025-12-12T17:35:45.804501025Z 304 GET /api/tree with 62585 bytes took 3ms
2025-12-12T17:35:45.809881858Z 200 GET /api/options with 9175 bytes took 2ms
2025-12-12T17:35:45.821204870Z 304 GET /api/keyboard-actions with 21860 bytes took 9ms
2025-12-12T17:35:45.826142491Z 304 GET /api/autocomplete/notesCount with 4 bytes took 2ms
2025-12-12T17:35:45.828759901Z websocket client connected
2025-12-12T17:35:45.857573344Z 304 GET /api/options/locales with 1113 bytes took 1ms
2025-12-12T17:35:45.901153233Z 304 GET /api/script/widgets with 2 bytes took 3ms
2025-12-12T17:35:45.979642244Z 304 GET /api/keyboard-shortcuts-for-notes with 2 bytes took 1ms
2025-12-12T17:35:45.983819215Z 200 POST /api/tree/load with 6485 bytes took 1ms
2025-12-12T17:35:45.986410944Z 304 GET /api/system-checks with 27 bytes took 1ms
2025-12-12T17:35:45.992506565Z 304 GET /api/sql/schema with 7987 bytes took 3ms
2025-12-12T17:35:46.002876098Z 304 GET /api/notes/18ZXLIxs4oza/blob with 207 bytes took 2ms
2025-12-12T17:35:46.049094791Z Slow 304 GET /api/recent-changes/undefined with 2 bytes took 10ms
2025-12-12T17:35:46.052841143Z 200 POST /api/tree/load with 4440 bytes took 1ms
2025-12-12T17:35:46.062793105Z 304 GET /api/search/note.parents.noteId%3D%2218ZXLIxs4oza%22%20%23!archived with 226 bytes took 5ms
2025-12-12T17:35:46.066569130Z 304 GET /api/notes/18ZXLIxs4oza/attachments with 2 bytes took 2ms
2025-12-12T17:35:46.069667287Z 304 GET /api/note-map/18ZXLIxs4oza/backlink-count with 11 bytes took 1ms
2025-12-12T17:35:46.073963997Z 200 POST /api/tree/load with 22719 bytes took 1ms
2025-12-12T17:35:46.107214162Z 200 POST /api/tree/load with 14474 bytes took 1ms
2025-12-12T17:35:46.131193500Z 304 GET /api/notes/root with 315 bytes took 0ms
2025-12-12T17:35:46.139787624Z 304 GET /api/search/%23textSnippet with 2 bytes took 2ms
2025-12-12T17:35:46.156043837Z 304 GET /api/search/%23workspace%20%23!template with 2 bytes took 2ms
2025-12-12T17:35:46.159092027Z 304 GET /api/notes/_template_text_snippet with 341 bytes took 1ms
2025-12-12T17:35:46.164182786Z 200 GET /api/autocomplete?query=&activeNoteId=18ZXLIxs4oza&fastSearch=true with 679 bytes took 2ms
2025-12-12T17:35:46.203934807Z 304 GET /api/notes/uypRCFCfQuCd/blob with 155 bytes took 2ms
2025-12-12T17:35:46.208070815Z 304 GET /api/notes/dEcu6nSi3wi1/blob with 155 bytes took 2ms
2025-12-12T17:35:46.214691577Z 304 GET /api/notes/2tdwxRTeYCkS/blob with 155 bytes took 2ms
2025-12-12T17:35:46.219717496Z 304 GET /api/notes/NRff3tmNriAt/blob with 155 bytes took 2ms
2025-12-12T17:35:46.224216381Z 304 GET /api/notes/lW6fjmHF9WSt/blob with 155 bytes took 2ms
2025-12-12T17:35:46.245566257Z 304 GET /api/notes/umycHZXo2h7Z/blob with 155 bytes took 2ms
2025-12-12T17:35:46.250410999Z 304 GET /api/notes/8AIkPfhcYGy3/blob with 155 bytes took 2ms
2025-12-12T17:35:46.254439873Z 304 GET /api/notes/28kp0BIcEpBC/blob with 155 bytes took 2ms
2025-12-12T17:35:46.260042906Z 304 GET /api/notes/tepEvw62HjXk/blob with 155 bytes took 2ms
2025-12-12T17:35:46.263741659Z 304 GET /api/notes/4M4DiZFXZhOT/blob with 155 bytes took 2ms
2025-12-12T17:35:46.267460606Z 304 GET /api/notes/92g0uLSsLmL2/blob with 155 bytes took 2ms
2025-12-12T17:35:46.271929355Z 304 GET /api/notes/5ofxaIBsl2AF/blob with 247 bytes took 2ms
2025-12-12T17:35:46.276938768Z 304 GET /api/notes/kPEpc3hp1ooN/blob with 155 bytes took 2ms
2025-12-12T17:35:46.280660403Z 304 GET /api/notes/kfQvtD1gx08m/blob with 155 bytes took 2ms
2025-12-12T17:35:46.284514113Z 304 GET /api/notes/iudDaClR20Z1/blob with 155 bytes took 2ms
2025-12-12T17:35:46.355160819Z 304 GET /api/notes/_template_list_view with 326 bytes took 0ms
2025-12-12T17:35:46.360426988Z 200 POST /api/tree/load with 5817 bytes took 1ms
2025-12-12T17:35:46.373140386Z 200 POST /api/tree/load with 11407 bytes took 1ms
2025-12-12T17:35:46.376951012Z 200 POST /api/tree/load with 6635 bytes took 1ms
2025-12-12T17:35:46.382758913Z 200 POST /api/tree/load with 6349 bytes took 1ms
2025-12-12T17:35:46.386332871Z 200 POST /api/tree/load with 3821 bytes took 1ms
2025-12-12T17:35:46.390844288Z 200 POST /api/tree/load with 6297 bytes took 1ms
2025-12-12T17:35:46.394513125Z 200 POST /api/tree/load with 14831 bytes took 1ms
2025-12-12T17:35:46.399294430Z 200 POST /api/tree/load with 10515 bytes took 1ms
2025-12-12T17:35:46.425187546Z 200 POST /api/tree/load with 7308 bytes took 1ms
2025-12-12T17:35:46.432783586Z 200 POST /api/tree/load with 4810 bytes took 1ms
2025-12-12T17:35:46.440888159Z 200 POST /api/tree/load with 3812 bytes took 1ms
2025-12-12T17:35:46.444841269Z 200 POST /api/tree/load with 17359 bytes took 2ms
2025-12-12T17:35:46.448069123Z 304 GET /api/notes/_template_grid_view with 326 bytes took 0ms
2025-12-12T17:35:46.497050623Z 304 GET /api/notes/_template_calendar with 324 bytes took 1ms
2025-12-12T17:35:46.517764624Z 304 GET /api/notes/_template_table with 318 bytes took 1ms
2025-12-12T17:35:46.531588014Z 304 GET /api/notes/_template_geo_map with 322 bytes took 1ms
2025-12-12T17:35:46.709122938Z JS Info: CKEditor state changed to ready
2025-12-12T17:35:46.734095524Z 304 GET /api/notes/_template_board with 325 bytes took 0ms
2025-12-12T17:35:46.752520756Z 304 GET /api/notes/_template_presentation with 332 bytes took 1ms
2025-12-12T17:35:46.764040101Z 304 GET /api/search-templates with 16 bytes took 2ms
2025-12-12T17:35:46.777169513Z 200 POST /api/tree/load with 5529 bytes took 1ms
2025-12-12T17:35:46.796644835Z 304 GET /api/notes/yivxnaKG7uTT with 332 bytes took 1ms
2025-12-12T17:35:46.934879828Z 204 PUT /api/options with 0 bytes took 9ms
2025-12-12T17:35:47.373764967Z Caught interrupt/termination signal. Exiting.

[doobes]

That was from Portainer.

This is from the log files:

17:45:02.470 📦 Versions:    app=0.100.0 db=233 sync=36 clipper=1.0
17:45:02.471 🔧 Build:       2025-12-05 10:24:54 (982fb212e4)
17:45:02.471 📂 Data dir:    /home/node/trilium-data
17:45:02.471 � UTC time:    2025-12-12 17:45:01
17:45:02.478 💻 CPU:         AMD PRO A6-9500E R5, 6 COMPUTE CORES 2C+4G (2-core @ 0 Mhz)
17:45:02.480 💾 DB size:     656.9 MiB
17:45:02.480 
17:45:03.026 Becca (note cache) load took 535ms
17:45:03.114 Updating attribute _help_Un4wj2Mak2Ky_ldocName from "User Guide/User Guide/Installation & Setup/Server Installation/Nix flake.clone" to "User Guide/User Guide/Installation & Setup/Desktop Installation/Nix flake"
17:45:03.136 Updating attribute _help_Un4wj2Mak2Ky_liconClass from "bx bx-file" to "bx bxl-tux"
17:45:03.156 Updating attribute _help_Un4wj2Mak2Ky_ldocName from "User Guide/User Guide/Installation & Setup/Desktop Installation/Nix flake" to "User Guide/User Guide/Installation & Setup/Server Installation/Nix flake.clone"
17:45:03.166 Updating attribute _help_Un4wj2Mak2Ky_liconClass from "bx bxl-tux" to "bx bx-file"
17:45:03.236 Trusted reverse proxy: 192.168.10.16
17:45:03.237 App HTTP server starting up at port 8080
17:45:03.248 Listening on port 8080
17:45:07.092 Table counts: notes: 1999, revisions: 650, attachments: 1639, branches: 2016, attributes: 2358, etapi_tokens: 0, blobs: 2974
17:45:07.338 Slow query took 231ms: SELECT id, entityId FROM entity_changes LEFT JOIN notes ON entityId = notes.noteId WHERE entity_changes.isErased = 0 AND entity_changes.entityName = 'notes' AND notes.noteId IS NULL
17:45:07.555 Slow query took 210ms: SELECT id, entityId FROM entity_changes LEFT JOIN revisions ON entityId = revisions.revisionId WHERE entity_changes.isErased = 0 AND entity_changes.entityName = 'revisions' AND revisions.revisionId IS NULL
17:45:07.592 Slow query took 24ms: SELECT id, entityId FROM entity_changes LEFT JOIN attachments ON entityId = attachments.attachmentId WHERE entity_changes.isErased = 0 AND entity_changes.entityName = 'attachments' AND attachments.attachmentId IS NULL
17:45:07.623 Slow query took 21ms: SELECT id, entityId FROM entity_changes LEFT JOIN blobs ON entityId = blobs.blobId WHERE entity_changes.isErased = 0 AND entity_changes.entityName = 'blobs' AND blobs.blobId IS NULL
17:45:07.860 Slow query took 223ms: SELECT id, entityId FROM entity_changes LEFT JOIN branches ON entityId = branches.branchId WHERE entity_changes.isErased = 0 AND entity_changes.entityName = 'branches' AND branches.branchId IS NULL
17:45:07.982 All consistency checks passed with no errors detected (took 933ms)
17:45:08.133 Sync failed: 'Request to GET https://trilium.danesburypark.com/api/setup/status failed, error: Error: write EPROTO 48828228EE730000:error:0A0000C6:SSL routines:tls_get_more_records:packet length too long:../deps/openssl/openssl/ssl/record/methods/tls_common.c:662:
', stack: Error: Request to GET https://trilium.danesburypark.com/api/setup/status failed, error: Error: write EPROTO 48828228EE730000:error:0A0000C6:SSL routines:tls_get_more_records:packet length too long:../deps/openssl/openssl/ssl/record/methods/tls_common.c:662:

    at Qv (/usr/src/app/main.cjs:49:3051)
    at ClientRequest.<anonymous> (/usr/src/app/main.cjs:49:1274)
    at ClientRequest.emit (node:events:508:28)
    at emitErrorEvent (node:_http_client:108:11)
    at _destroy (node:_http_client:962:9)
    at onSocketNT (node:_http_client:982:5)
    at process.processTicksAndRejections (node:internal/process/task_queues:90:21)
17:45:21.837 ERROR: WebSocket connection not allowed because session is neither electron nor logged in.

[eliandoran]

@doobes , did you remove the trailing slash (http://192.168.10.17:8080 instead of http://192.168.10.17:8080)?
Either way, from this log 2025-12-12T17:35:47.373764967Z Caught interrupt/termination signal. Exiting. we can tell that the server is closed by some external entity, most likely Traefik?

[doobes]

OMG. That was it.... Sort of. Now it's stuck on a specific record.

Why would traefik be shutting trilium down?

[eliandoran]

Now it's stuck on a specific record.

It will take some time. At some point, if you have many notes it might timeout. All you have to do in that case is to close and restart Trilium. It will resume from where it left off.

Why would traefik be shutting trilium down?

No idea.

[doobes]

Ok, it's done. Had to stop and restart several times.