Re: [raxml] RAxML Problem Reading Alignment File

[Alexandros Stamatakis]

please specify the comman line parameters you have been running & send
me the alignment file as well as the name of the outgroup, it's very
hard to answer abstract questions like these,

Cheers,

Alexis

On Thu, 2012-10-04 at 15:44 -0700, Elizabeth wrote:
> Hi all, I'm a new user of RAxML with no more experienced users available to
> help me through the rough patches. I have a concatenated file of three DNA
> sequences, saved in Phylip format. I'm trying to run a preliminary ML
> search but keep getting an error msg: Could not read data: Problem reading
> alignment file. With no more information than this, I'm at loss of how to
> approach this problem.
>
> I ran it on RAxML Black Box on Cipres, and received an error message that
> my outgroup was not found. I have double-checked and indeed it is there.
> Can anyone offer any suggestions as to what else I might try?
>
> Thanks.

--
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

[Mark Miller]

Or, alternatively, you can send me the job handle for your failed cipres job (if it failed in the past 3 weeks)

Here is how to find it:

http://www.phylo.org/index.php/help/report_failed_job

 

I will have the files and can help trouble shoot.

 

Best,

Mark