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rrwick / Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes
GNU General Public License v3.0
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MUSCLE version compatibility issue? #38

Closed fgaudilliere closed 2 years ago

fgaudilliere commented 2 years ago

Hi there!

First of all, thank you for all the work you put into making Trycycler and all your other tools as easy to use as possible.

I just wanted to let you know that I ran into an issue trying to use Trycycler with the latest version of MUSCLE. The default version on my lab's cluster is version 5.1, and it seems to mess up the trycycler msa step. I kept getting the following error:

Error: MUSCLE failed to complete on 4988 of the 4988 pieces. Please remove the most divergent sequences from this cluster and then try again.

I solved it by loading MUSCLE v.3.8.31 instead.

Best, Flora

rrwick commented 2 years ago

Hi Flora,

Are you using the latest version of Trycycler? I updated it in v0.5.2 to work with MUSCLE v5, and I just double checked on two computers (my Mac laptop and a Linux server), and it seems to be working (for me anyway).

That being said, MUSCLE v3 seems to be much faster than MUSCLE v5, so you might want to stick with the older version anyway. See more here: https://github.com/rrwick/Trycycler/wiki/FAQ-and-miscellaneous-tips#a-note-on-muscle-versions

Ryan

fgaudilliere commented 2 years ago

Hi Ryan,

I checked, and our version is v0.5.0, so this explains that. Thanks for the clarification! (Sorry, I hadn't read that part of the wiki)

Best, Flora