lh at root is not a number

[stitam]

Hi, I have a tree of approx. 5000 bacterial genomes. I created this tree using a software which returns a tree and a masked alignment. I used these files to run root digger and received the following error: terminate called after throwing an instance of 'std::runtime_error' what(): lh at root is not a number: nan. When I draw a random subsample of 100 from both the tree and the alignment, root digger completes successfully. Do you have any idea what might be causing the error and how to fix it?