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SorenKarst / longread_umi

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Nanopore pipeline fails when specifying medaka model r103_hac_g507 #47

Open thekatpod opened 2 years ago

thekatpod commented 2 years ago

Hello, thanks for a great contribution to the ONT community. I'm having issues with the pipeline failing because it seems like it's using an older version of medaka which does not include the new models for Guppy version 5.0.7. I've basecalled my data using Guppy 5, so I'd like to use a corresponding medaka model. Could this be updated or am I doing something wrong? I am unsure what the consequences of polishing with medaka using a model based on 3.4.5 when I've basecalled with 5.0.7. Thanks in advance!

SorenKarst commented 2 years ago

Hi,

Thank you.

It is using an older version of Medaka, but it might work if you try to update it manually.

Install the development version of the pipeline: https://github.com/SorenKarst/longread_umi/tree/develop

Run the following code

conda update -n longread_umi medaka

Let me know how it goes.

regards Søren

thekatpod commented 2 years ago

Hi Soren. Thanks so much for you response. I downloaded the developer version, and it installed fine, ran tests etc. and all good. I ran the update code, but the version of Medaka is still 1.0.1 unfortunately.

SorenKarst commented 2 years ago

The newer versions of medaka has some dependencies that clashes with the some of the older packages used in the pipeline.

I will look at a fix.

cfblaeb commented 2 years ago

Upgrading the dependencies to work with newer models would very much be appreciated

MaestSi commented 10 months ago

Hi @thekatpod and @cfblaeb , please have a look at this post for testing a longread_umi-inspired pipeline with updated dependencies. SM