Hi Ben!

I wrote a script to cluster 522 dereplicated MAGs into 329 species clusters (inspired by https://www.nature.com/articles/s41587-020-0501-8). As my algorithm is quite similar to Galah's, I also tried to use it to see if the results would be similar:

galah cluster -t 64 --quality-formula Parks2020_reduced --checkm-tab-table dereplicated_mags_CheckM.txt -f Dereplicated_mags/* --prethreshold-ani 0 --ani 95 --min-aligned-fraction 60 --output-cluster-definition clusters.txt

Unexpectedly, Galah generated 418 clusters. I noticed that there are some MAGs that have more than 97% ANI and more than 90% aligned fraction (according to fastANI) that were not clustered.

What might be going on here? I'm I using some parameter wrong?