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Can I eject the flow cell MinION from USB port when doing basecalling? Because its taking long and its not possible to wait for its finished, will it affects basecalling?

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You can, you will lose the transfer from the MinION. It would probably be better to just stop the run. The computer will continue to basecall untill it is done. All the raw reads are stored locally on the machine so it should be fine.

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Yes, it should be fine, especially if the run is finished. MinKNOW should still continue basecalling even after the MinION is disconnected. Unfortunately I can't find good posts in the ONT community about that because search is currently broken. This post might be useful (found by searching my email records), but it's two years old:

Hi, thank you for your post. You can certainly remove the flow cell and wash it without affecting the catch-up mode. Please see the downloads page here for the most up-to-date installer version.
- Monolina Binny, ONT

If you're likely to be doing more long runs in the future (>6h), I'd recommend getting a cheap video card with CUDA capability (at least v10) to save time in the future.

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