this is an error in IQtree (seg fault). Hard to say what is causing it. How big is your tree?
@rneher Used the full GISAID data, my last build ended with around 1200-1400 sequences in the tree, but ran all the way through just fine. My current build should be basically same size.
this is either a problem with IQtree (in which case I don’t think we can help much), or there is something weird with the alignment that goes into the tree. I would inspect the alignment for any hints.