Codeml error - format problem?

Question

[natasha]

Hi

I am having problems trying to get codeml to run. I have read through all the other posts for similar issues on biostars and tried everything I can think of. I am inputting a tree (newick format) and a gene alignment of the coding regions for 57 bacterial isolates (phylip format), as well as a .ctl file.

Firstly I tried reformatting my gene alignment/phylip in every way possible - so I think I've ruled this out as the issue. So I guess the error may be because of stop codons? I really don't understand why I would have stop codons in my alignment, would anyone be able to help?

This is the error message that appears:

stop codon TGA in seq. #   1 (04-2549_Canada_2004)_2009)2004)
53124 columns are converted into ??? because of stop codons
Press Enter to continue

codon 1227474: TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA AGC TCA TCA TCA TCA AGC TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA AGC TCA TCA TCA TCA TCA TCA TCA TCA TCA 59 ambiguous codons are seen in the data:
 --- --A --C --G --T -AA -AG -AT -CA -CC -CT -GA -GC -GT -TA -TT ??? A-- A-G AA- AC- AG- C-- C-T CA- CC- CG- CT- G-- G-T GA- GC- GG- T-- TA- TC- TG- TT- AT- -AC C-G -GG G-C NTG NNN NNT ANN CNN TNN GNN NAG NGA NCG CTN NCC --N A-C NAT GT-


  12768 bytes for distance
 7590352 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

TREE #  1

208734680 bytes for conP, adjusted

ntime & nrate & np:   111     2   113

Thanks

Answer 1

[rstuder]

Dear Natasha,

You probably have found a solution, but it looks like you are giving whole genome (isolate) to CodeML (as "53124 columns" seen in the output). But CodeML requires protein-coding sequences to work at best.

Best regards, Romain