snp-sites -c doesn't produce recognisable alignment for IQtree about snp-sites HOT 1 OPEN

Hi! IQ-TREE dev (well, kinda, I sort of help a bit) here. This looks like an IQ-TREE issue not an issue with snp-sites.

Can I suggest you post this issue here: https://github.com/iqtree/iqtree2

While you do that - can I ask what value you supplied as [fconst_param]?

Your commandline looks like this (from your log file):

iqtree -fconst fconst_param -s core.full.snp-sites_filtered.aln

My guess from looking at the stack trace is that this is related to the issue you're getting. It's hard to know for sure if this is the issue (mostly because I'm too ignorant), but -fconst expects a list of integers like this:

-fconst 10,20,15,40

from the docs: "IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment."

Rob

from snp-sites.