Open thekatpod opened 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
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.
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.
Upgrading the dependencies to work with newer models would very much be appreciated
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!