nickjcroucher

What's the command you're using?

Sorry, daft mistake now fixed in 4581de1ee1436d68dd4357e53f60d2f485582983 - if you can clone the repo and run a local install, that should fix the problem

@yuanw-18 I can't remember if this is possible in versions < 3, but you can try using the Jukes-Cantor or K2P models to avoid having to estimate empirical base frequencies....

The forward and reverse FASTQs need to be on the same line. e.g.: `JSAHVC01R1 /home/work/APECSRA/JSAHVC01R1.fastq /home/work/APECSRA/JSAHVC01R2.fastq` I should allow for single FASTQ files generally though.

It's a small change to the search strategy for recombinations - by default, Gubbins will use a threshold number of SNPs to identify recombinations. This used to sometimes be higher...

Hopefully fixed and tested in 359c16c, will update when when included in a new release.

This is just a warning, the output should be fine unless there is another error - we will update this code soon.

I think this is due to a Biopython upgrade - what version are you using?

Just an FYI - Gubbins requires python version >=3.8 for parallelisation. Did you install with conda - and what happens if you use a more recent python version?

Phew! Great, glad it's working now.