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Could be a disk Io issue. I know git used to use a nieve approach on windows and it make git incredibly slow. Something you wouldn't notice just using git but when you made it part of your prompt it would lag for a good second and a half just pressing enter.

Are you on ZFS by any chance? There's a bug with SQLite which can lock the thread for a few seconds, I had the same problem. Here's the issue I created, with several workarounds included. My current workaround is to have a separate dataset without sync for the atuin directory.

https://github.com/atuinsh/atuin/issues/952

Yup, I'm getting this sometimes on Linux.

There's been a recent update (not sure which version, I don't have my Linux box on hand to check) where it now started logging some timeout waiting for a lock on the database.

I don't type commands in multiple shells at the same time, so not sure what's locking the db. I also don't use remote sync (explicitly disabled in the config).