mauveAligner outputs empty .mauve files and no .alignment files

Question

[langziv]

Hi.

I'm running mauveAligner with 2 genomes from the same species that might belong to 2 different strains. I'm also getting an error message: Clust::SetLeafCount(0).

/mauveAligner --output=genomes1_2.mauve \
--output-alignment=genomes1_2.alignment \
/output/mauve/genome1.fa /output/mauve/genome1.sml \
/output/mauve/genome2.fa /output/mauve/genome2.sml

Any ideas why that's happening?

Thanks.