Low quality genomes end up as seperate species.

[SilasK]

Low-quality genomes cluster apart. I used galah on large datasets. What I noticed is that often a low complete genomes are selected as separate species, which are then annotated by GTDB-tk as the same species as other high-quality genomes.

I have the impression that if a genome has low completeness it will not pass the min coverage of FastANI and so yield no FatANI report. I don't know how you do this internally but I imagine they perturb the clustering.

Would the solution simply be to use a very low --min-aligned-fraction?