Marcus Stoiber

@AlexdeMendoza , @nmierzam , @marcDabad This looks potentially like a regression in guppy 6.1.* on rerio models. Could you try to run megalodon on a standard canonical model to confirm...

There is an all-context 5mC Remora model (only kit14 atm) in Rerio. We are working very hard to get a 6mA all-context Remora model released as soon as possible.

In terms of all-context mods for R9.4.1 at the moment the Rerio model is the best option, the guppy devs will have a look at this next week as this...

I would admit that the development of megalodon has outstripped the documentation. I would be more than happy to review a pull request with documentation updates (even minor documentation updates...

I'm not sure I understand what you are trying to do. Can you give the commands that you have run and the desired output?

It looks as though there is an error overwritten by the progress bars. Could you post the end of the log.txt file produced?

This appears to be an issue with accessing the database file on disk. Can you try the `megalodon_extras modified_bases index_database` command on the output directory?

This is not currently implemented. There is a bit of logic that needs to be filled in to enable variant calling on RNA/3’ to 5’ signal direction reads. This is...

We are working to deprecate megalodon at the moment. Are you able to run this basecalling model from Guppy standalone?

Remora modified base calling has been included in Guppy since [version 6.1.1 (March 2022; login required)](https://community.nanoporetech.com/posts/guppy-v6-1-1-release) and will be in Dorado (replacement for Guppy) shortly. So yes the idea is...