Suddenly receiving database error message

571288research · 2025-10-17T13:57:59+00:00

Report ID: 1224034391

Really hope someone can help. I haven't made any changes to the location of Zotero on my local machine for about 10 days. Can see that my online backup has updated a few minutes ago but getting an error describing a database corruption error and that last back up was about five hours ago.

I'm a little confused. Is the simplest fix to scrub Zotero and reinstall?

dstillman · 2025-10-17T14:04:32+00:00

database disk image is malformed

Your database appears to be corrupted. Do you have your data directory on the local disk, or is it somewhere else (e.g., a network drive or a cloud storage folder)? The latter would be the most common cause.

You can try restoring from one of the automatic backups, or, depending on the size of your database, you can try the DB Repair Tool. (You can also open the database with sqlite3 and run PRAGMA integrity_check; to confirm that it's actually corrupted.)

571288research · 2025-10-17T14:13:23+00:00

Full message: The Zotero database “zotero.sqlite” appears to have become corrupted.

This generally occurs when the Zotero data directory is stored in a cloud storage folder or on a network drive. If you’ve moved your data directory to one of those places, you should move it back to the default location.

Zotero can attempt to restore from the last automatic backup from 10/17/2025 at 9:57:57 AM.

For more information on repairing or restoring the database and preventing further corruption, see https://zotero.org/support/kb/corrupted_database

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I am able to access the sqlite file and can see my latest annotations have been saved there.

571288research · 2025-10-17T15:12:52+00:00

Hi dstillman, I have both, zotero.sqlite locally and syncing using WebDav with koofr.net.

dstillman · 2025-10-17T15:21:31+00:00

No, this is about the location of your data directory, not anything related to Zotero file syncing.

dstillman · 2025-10-17T15:23:45+00:00

(Unless you actually mean that you have zotero.sqlite in a WebDAV-synced folder, in which case that's how you corrupted it.)

571288research · 2025-10-17T15:27:32+00:00

Thanks. The data directory location has not changed today, but the error has started today. zotero.sqlite is local. Haven't touched either the sqlite file or WebDav settings today. Can view the sqlite file and see new records are being made as I am making new annotations.

dstillman · 2025-10-17T15:28:27+00:00

One way or another, your database is corrupted. See my response above. Nothing really else to say here.

571288research · 2025-10-17T15:28:35+00:00

Koofr last synced about two hours ago.

dstillman · 2025-10-17T15:29:13+00:00

(And note that the corruption could have happened at some point in the past and just been triggered today.)

571288research · 2025-10-17T15:29:58+00:00

OK, thanks. Guess I was puzzled as to why it was triggered today.

dstillman · 2025-10-17T15:30:42+00:00

But I'm unclear why you keep mentioning Koofr? Again, if you're talking about Zotero file syncing, it has absolutely nothing to do with that. If you're using Koofr to sync files outside of Zotero, including zotero.sqlite, that's how you corrupted the database.

571288research · 2025-10-17T15:40:08+00:00

Your latest answer is confusing and convoluted. I will try and follow the advice you provided above.

I tried to provide as much information as I could, hence, my mention of koofr which suddenly stopped syncing about two hours ago. I have used it for two years with no issue.

I have, however, made changes to the location of some Zotero files locally about ten days ago which possibly explains this issue. But the fact that the sqlite is being updated as I continue to work confused me.

The reason I mentioned Koofr file syncing...
https://s3.amazonaws.com/zotero.org/images/forums/u13850071/v5lu9zkpgog59bcmkh14.png

dstillman · 2025-10-17T15:49:51+00:00

As I say, a corrupted zotero.sqlite database has nothing to do with WebDAV syncing within Zotero. It's your Zotero database, not a Zotero attachment file.

571288research · 2025-10-17T16:02:35+00:00

Thanks. I was confused that it was saying corrupted database, but the database seemed to be working in the sense that new records were being added. And confused that koofr was not syncing despite being seemingly unrelated to the issue reported.

dstillman · 2025-10-17T16:04:28+00:00

Corruption often only affects part of a file, so only some operations might be affected. That's also why might not see an error immediately.

571288research · 2025-10-17T16:11:54+00:00

Yes, I was thinking the same thing.