I am trying to calculate unifrac beta diversity. I used the SGB tree in the Newick format, but I received the error messages. PS: I had no issues calculating other alpha and beta diversities.
Thanks!
Error in FUN(X[[i]], …) : attempt to set index 0/0 in SET_STRING_ELT
Calls: → lapply → FUN
In addition: Warning message:
In FUN(X[[i]], …) : NAs introduced by coercion
Execution halted
I had this problem myself a few days ago.
Are you using the most recent tree “mpa_vOct22_CHOCOPhlAnSGB_202212.nwk”?
In my case I was using the tree from Jan21.
I tried both nwk version, and got the same error messages. : (
Hi @anitalijia which metaphlan database version are you using when running metaphlan?, you can check it in the first lines of your profiles
Hi @aitor.blancomiguez : I used mpa_vJan21_CHOCOPhlAnSGB_202103.nwk, and my metaphlan used the same version. I am still experiencing issues with it.