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mask_gubbins_aln.py issue
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
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!
I think this is due to a Biopython upgrade - what version are you using?
Hi Nick,
Thanks for quick reply!
I've tried v1.76 and v1.78.
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?
Solved! Tried later version of python and it works great!
Phew! Great, glad it's working now.