Ask about simuliation without Minknow device

[ElroyLR]

Hello， I'm looking forward to running readfish on some samples,So I tested the fast5 file provided. According to the description in the readme.md file, an attempt was made to add [custom_settings] and 'silumination='my/path/to/fast5' to the accompanying toml file in the repo, but an error occurred:

😾 This TOML file has failed validation See below for details:
Additional properties are not allowed ('custom_settings' was unexpected)

Then I modified the 'ru/static/readfish_toml. schema. json' file, but I couldn't customize the format of the toml file, and the above error still occurred.

So I have some questions,

1. How to solve this problem？
2. Can readfish use fast5 files for testing without connecting to Minknow devices?
3. Do I have to use the sever version of Guppy to apply to readfish? Can Guppy installed locally be supported?

Have a good day. Looking forward to your reply.

[mattloose]

Hi,

You have edited the wrong toml file to add the [custom_settings] too. You should be editing one of the sequencing configuration files (also TOML files) that are installed when you set up MinKNOW.

So to address your questions in turn.

1) - You can solve this problem by installing MinKNOW and configuring a simulation minION if you wish (look on the ONT forums to do this). 2) - No - readfish cannot itself playback fast5 files. We do have a separate tool - ICARUST - that will allow you to do this - see https://www.biorxiv.org/content/10.1101/2023.05.16.540986v1 for more information. 3) - This is confusing nomenclature. Guppy runs locally in all cases - even when we run guppy server. So this is a local installation of guppy on your local machine but it runs in server mode. I hope this helps.

[github-actions[bot]]

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[mattloose]

Closing as stale.