In format_tree(args$tree) : NAs introduced by coercion

[jellyvanderwoude]

Here's the code I'm running:

hogwash(pheno = AK, geno = genotype3, tree = phytree, tree_type = "phylogram", file_name = "gene_presence_absence_hogwash", dir = "~", perm = 10000, fdr = 0.15, bootstrap = 0.95)

and this is the error I get:

Error in if (num == Inf | num == -Inf) { : missing value where TRUE/FALSE needed In addition: Warning message: In format_tree(args$tree) : NAs introduced by coercion

It seems like something's wrong with my tree... my tree is unrooted (expecting Hogwash to do it for me), I created my tree using PIRATE and read in my tree using treeio:

phytree <- read.tree("core-genome.treefile")

I've attached a screenshot of my tree file as plotted using ggtree: