mask_gubbins_aln.py not removing recombinant regions about gubbins HOT 9 CLOSED

What version are you using, and what is the command you are running?

from gubbins.

Are there any unusual characters in your isolate names (e.g. "#"?)

from gubbins.

Are there any unusual characters in your isolate names (e.g. "#"?)

Same issue with Erin.
The mask aln is as same large as input aln.
The isolate name has "." and "_".

from gubbins.

Python: 3.11.7 Biopython: 1.82
The command: python3.11 /data4/CLC_data4/shiqiucheng/software/mask_gubbins_aln.py --aln clean.full.aln --gff clean.full.recombination_predictions.gff --out clean.full.mask.aln
recombination_predictions.gff file has 1457 lines of predictions.

from gubbins.

Thanks - what version of Gubbins?

from gubbins.

gubbins 2.4.1

from gubbins.

Try upgrading to the latest version (3.3.2)

from gubbins.

How does the recombination removal fragment show in the alignment file, replace by "_" or "N"?
Because byte count of clean.full.aln and clean.mask.aln are identical, but the counts of ATCG are different.

from gubbins.

Whatever you set the missing character to - by default it is - - this is documented in the script's help.

from gubbins.