Error when trying to constrain through binary backbone

[Ana Otero]

Hi,

I was trying to run a constrained analysis like this:

raxmlHPC-HYBRID-AVX -T 4 -f a -N autoMRE -n result -s infile.txt -c 25 -m GTRCAT -p 12345 -r binary_backbone.tre -x 12345 -o Nuphar_luteum_luteum,Nymphaea_alba This is a matrix of 4703 taxa concatenating two molecular markers (2076 positions) and a binary tree in newick format including 888 taxa.

I get this error:

RAxML could not find a single "(" in what is supposed to be your tree file
RAxML will exit now, please check your tree file!
The last couple of characters RAxML read in your supposed tree file look like this:

------T-------CA---------------------------------

I don't know exactly where is the error. I have checked tip names for the binary tree and newick format and I think it's formatted properly. 

Could you help with this?

Thank you a lot,

Ana.

[Alexandros Stamatakis]

Can you send me your tree file please? It looks as if your tree fiel
contains DNA data.

Also, please consider switching to the latest RAxML version, RAxML-NG:

https://github.com/amkozlov/raxml-ng

Alexis

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Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Ana Otero]

OMG, This is terrible, I'm so sorry Alexandros. I just realized this was all a misunderstanding. I was uploading the nucleotide matrix as the binary backbone! Now with the actual tree the analysis ran perfectly. Also I'm trying RAxML-NG.

I really appreciate your quick response. 

Thanks a lot!

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Ana Otero Gómez, PhD

Universidad Autónoma de Madrid.

Facultad de Ciencias. Departamento de Biología (Botánica).

Calle Darwin, 2 28049 Madrid. Spain