Issues with input tree

[Avehi Singh]

Hi all,

I've been having some issues with the input files for PAML site models (I have attached my codon file, tree and codeml.ctl files below).  I am using PAML 4.9 on Ubuntu 22. Running codeml on the tree and codon file produces this (clipped) error message:

Sites with gaps or missing data are removed.
28 ambiguity characters in seq. 46
10 sites are removed.  233 234 235 236 237 238 239 240 241 242
Sequences read..
Counting site patterns..  0:00

Counting codons..
    12768 bytes for distance
   403088 bytes for conP
    36344 bytes for fhK
  5000000 bytes for space

Model 0: one-ratio
Seq #51 (Obicornis_bicornis) is missing in the tree

The sequence above is, in fact, in the tree, so I can't figure out why PAML can't parse it. I've tried several troubleshooting measures over the last few days but so far, nothing has worked. This is what I've tried so far:

- ensuring that the sequence names in the tree and codon file were the same

- checking for line ending characters (CF and LRF) -- all files are in ASCII 

- removing branch lengths from the phylogeny

- checking sequence lengths of the codon file match (they are 1278 characters long)

Could anyone help me figure out what I'm doing wrong? 

Thank you so much in advance,

Avehi 

[Janet Young]

it looks like Obicornis_bicornis is present twice in your alignment file - that is most likely the issue

[Avehi Singh]

Thank you so much! I changed the labels of the duplicate sequences and this worked!