BayesTraits Error: Does have a translate line

Question

I am running a test on behavioral evolution, using the multistate function of BayesTraits v. 4.0.0. I have my rooted treefile Tree.trees (using FigTree), my list of specimens in a .txt like like below:

Sp_1 AC
Sp_2 E
Sp_3 ABD
...
and so on
*There are over 300 specimens included in my phylogeny, 
and some have multiple behavioral patterns recorded for a single species, 
relating to the multi-lettered samples such as Sp_3 doing three behaviors (ABD). All are tab deliminated.

and an Input.text as

1
2
Run

My files look the exact same as the example files, but when I try to run this in command line on a Mac OS,

./BayesTraitsV4 Pomp.trees Pomp.txt < PompIn.txt

I get

Err: Does have a translate line

I have not found any information about this error, what it means, or how to fix it. I hope someone could give some guidance, thank you!

Answer 1

Yep, that's right. Trees in nexus format without a translate table will produce that error. Instead of editing the tree file manually, I have found that importing the trees in R with ape::read.nexus() and then exporting the trees with phytools::writeNexus() will get your tree(s) in the right format.