Bad Base, I,L,F,P,Q,E

[gaby_...@hotmail.com]

Hi,

I used RAxML -7.2.7-ALPHA, input datei is protein sequences, and I got the erro message,
ERROR: Bad base (I) at site 4 of sequence 1

After I deleted all "I", I got new erro message,
ERROR: Bad base (L) at site 36 of sequence 1

I deleted all "L",   then erro message about characters, F,P,Q,E. After I removed all these characters, the program ran very well.

I think, that I have the correct input format, but the characters  I,L,F,P,Q,E are not allowed in the input sequences.
But what should I do with these characters?

Best
gaby

[Fidel Botero]

Do you have any spaces in your taxon names ? Try replacing them with underscores \ _ \, it thinks a problem when reading names.

Best,

Fidel

2013/8/27 <gaby_...@hotmail.com>

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Fidel Botero
Biologiste
Doctorant Université Montpellier 2
Équipe Phylogénie et Évolution Moléculaires
Institut des Sciences de l'Évolution de Montpellier - ISE-M (UMR 5554 UM2-CNRS)
04 67 14 92 00

[gaby_...@hotmail.com]

Hi, Fidel,

I dont have spaces in the taxon names, the taxon names like "Cp-ABC32_2".
best

[Fidel Botero]

Could I give a look at the file?

2013/8/27 <gaby_...@hotmail.com>

[J.M.P. Alves]

Which model did you specify to the -m parameter? It sounds like RAxML
is thinking your sequence is DNA (and therefore accepting only IUPAC
nucleotide chars, like W, B, S, etc.)

I hope that helps.
Cheers
J

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
João Marcelo Pereira Alves (J), PhD
Genomics, Molecular Phylogeny and Evolution

[Alexandros Stamatakis]

Dear Gaby,

Please note that, we also need you to provide the command line you used
to run the program in order to help.

The most up-to-date RAxML version is available on github by the way.

https://github.com/stamatak

Alexis

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[gaby_...@hotmail.com]

Hi, Alexis and Fidel,

thanks a lot!!! I got the problem, I have protein sequences and I used -m GTRGAMMA!
The program thougth that I had IUPAC nucleotide chars, and  showed erro messages for every character of "I,L....."

Best
Gaby

[Heiko]

Dear Gaby,

RAxML has no other choice than to interpret your sequences wrongly as DNA, because GTRGAMMA is a DNA model. Please choose a protein model to continue.

Best wishes,
Heiko