Re: [raxml] SNP Tree using asc-corr on CIRPRES

[Alexandros Stamatakis]

On 02.08.2016 15:56, Brendan Pinto wrote:
> Hi all,
>
> I am trying to run RAxML with the stamatakis ascertainment bias
> correction (asc-corr=stamatakis) on the CIPRES server (RAxML-HPC v.8 on
> XSEDE) and continue to repetitively get this error.
> "
>
> This is RAxML Worker Pthread Number: 3
> You specified that you want to use a stamatakis or felsenstein ascertainment bias correction for partition 0 with name p1.
> but did not specify a correction file for this partition in the partition file!
>
>
> "
> I know this is not true, but I don't know how to fix it. I only have one
> partition for my unlinked SNPs and a corresponding correction file. I am
> doing something wrong, but frustration is getting the better of me.

well in that case, you need to pass this partition file just containing
the description of a single partition via the -q option to RAxML ...

alexis

>
> Has anyone else had a similar issue?
> Thanks in advance!
> -bjp
>
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--
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

[Brendan Pinto]

Hey Alexis, Thanks for your reply!

It turns out it was a mixture of my ignorance and a CIPRES server issue. 

For the exciting conclusion to this issue please reroute: https://groups.google.com/forum/#!topic/cipres-science-gateway-users/GhF_efn8kvo 

Best,

bjp

[Alexandros Stamatakis]

great :-)

alexis

> > an email to raxml+un...@googlegroups.com <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.

> > For more options, visit https://groups.google.com/d/optout

> <https://groups.google.com/d/optout>.

>
> --
> 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 <http://www.exelixis-lab.org>