IQTree ERROR: Numerical underflow (lh-branch

[aldendirks]

Hello,

I am running into an issue with a 47 genomes, 874182 columns dataset. When I attempt to run this pipeline I get an error from IQTree that shuts down the supermatrix analysis:

ERROR: Numerical underflow (lh-branch). Run again with the safe likelihood kernel via -safe option

I've gone into the python script and attempted to add the -safe option where I saw iqtree commands. I hope this works. Maybe there could be an option to set iqtree to -safe when running the python script?

Thanks!