unique.fn.list is not made but *.an.list

I was trying Analyzing H1N1 swine-origin Influenza A isolates
I cant give the command mothur > read.otu(list=HA.unique.fn.list) as the list file produced produced is *.an.list, (and read.otu is obsolete) Is this happening normal

fn is for furthest neighbor and an is for average neighbor. a while back we switched to using an as the default since it is better than fn. the read.otu functionality has largely been replaced by make.shared.