mask_gubbins_aln.py issue

[Dangoh]

Hi,

I have problems running mask_gubbins_aln.py and get an error saying:

Traceback (most recent call last): File "mask_gubbins_aln.py", line 71, in taxon.seq = MutableSeq(taxon.seq) File "/opt/rh/rh-python36/root/usr/lib64/python3.6/site-packages/Bio/Seq.py", line 1663, in init "The sequence data given to a MutableSeq object "

My input is basically the alignment I had for gubbins in .fasta format and the .gff from gubbins as below:

python3.6 ~/tools/gubbins/python/scripts/mask_gubbins_aln.py --aln /mnt/eg/gubbins/eg_13-20/all_eg.fasta --gff /mnt/eg/gubbins/eg_13-20/all_eg_gubbins.recombination_predictions.gff --out /mnt/eg/gubbins/220824_gubbins_aln.fasta

Any ideas what the issue might be?

Thanks in advance!

[nickjcroucher]

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

[Dangoh]

Hi Nick,

Thanks for quick reply!

I've tried v1.76 and v1.78.

[nickjcroucher]

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?

[Dangoh]

Solved! Tried later version of python and it works great!

[nickjcroucher]

Phew! Great, glad it's working now.

[sylarKYG]

Solved! Tried later version of python and it works great!

Hi Dangoh,

What version of python and biopython did you use, same issue with you.