'Problem reading number of species and sites'

[Alice2430]

Hi,

I'm (very) new to using RAxML and have been trying to run a RAxML analysis but I keep getting the error message 'problem reading number of species and sites'. I have double checked the number of species and sites in my alignment and they match the information at the top of the file so I'm not quite sure where I'm going wrong?! Any help would be very gratefully recieved,

Thanks 

Alice

[Fidel Botero]

Hello Alice,

A frequent mistake is to include spaces in the species' name. RAxML reads the first space as the separator between taxa name and sequence, so every character after this space is considered as a nucleotide/aminoacid. Maybe this is your case ?

Hope it's useful !

Fidel

2012/8/9 Alice2430 <funky....@gmail.com>

--
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

[Alexandros Stamatakis]

thanks Fidel, that may be one cause.

Alice, please also have a look at the relaxed phylip format
specification in the old raxml manual:

http://sco.h-its.org/exelixis/oldPage/RAxML-Manual.7.0.4.pdf

Alexis

On Thu, 2012-08-09 at 15:47 +0200, Fidel Botero wrote:
> Hello Alice,
> A frequent mistake is to include spaces in the species' name. RAxML reads
> the first space as the separator between taxa name and sequence, so every
> character after this space is considered as a nucleotide/aminoacid. Maybe
> this is your case ?
>
> Hope it's useful !
>
> Fidel
>
> 2012/8/9 Alice2430 <funky....@gmail.com>
>
> > Hi,
> >
> > I'm (very) new to using RAxML and have been trying to run a RAxML analysis
> > but I keep getting the error message 'problem reading number of species and
> > sites'. I have double checked the number of species and sites in my
> > alignment and they match the information at the top of the file so I'm not
> > quite sure where I'm going wrong?! Any help would be very gratefully
> > recieved,
> >
> > Thanks
> > Alice
> >
>
>
>

--

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

[Alice2430]

Hi,

Thanks for the help, I've been through the sequence names and I have no spaces, but some of the names were exactly 10 long meaning they ran straight into the data matrix which I think may have been causing the problem. It seems to be running now :)

Thanks again for the prompt responses

Alice

[Ramona Walls]

Another common problem is having more than one blank space after your taxon name in the phylip file.

Ramona

[Alexandros Stamatakis]

That's actually not a problem in RAxML as it can parse the relaxed
PHYLIP format that allows for this (i.e., several spaces after the taxon
name).

Alexis

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[Ramona Walls]

RAxML can handle it fine, but parser (as part of ExaML) gives the error message.

[Alexandros Stamatakis]

That should not be the case with ExaML either, can you provide an
example where this happens?

Alexis

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> <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
>

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

[Ramona Walls]

I downloaded ExaML 3.0.20 (latest as of a few weeks ago), compiled parse using Makefile.SSE3.gcc (on Stampede2 on TACC), and tried to run it on a file that had two spaces after the model column, as below:

DNA,  Subset1 = 1-238

DNA,  Subset2 = 239-520

DNA,  Subset3 = 521-1689

...

I got the error message about  'problem reading number of species and sites'. When I removed the extra spaces, it worked fine.

I can't share the input files here as they aren't my data, but if you'd like, I can email them to you.

Ramona

[Alexandros Stamatakis]

okay I see thanks, that's not a problem in the alignment file (that's
what I understood) but with parsing the partition file ... now it's
clear, no need to send me the files ...

Alexis

[Maryam]

Hi,

I have an alignment file which I used it to infer a tree using RAxMl and I did not get any error. Now I am going to use ExaML on this alignment, but I keep getting this error: "problem reading number of species and sites". I should mention that I do not have any space in the names of the specious.

Thanks,
Mary

[Alexey Kozlov]

Hi Mary,

if I recall it correctly ExaML parser supports PHYLIP alignments only.

So could you please check and if necessary convert your alignment to PHYLIP (e.g. using the convertFasta2Phylip.sh
script shipped with RAxML).

Best,
Alexey

[Maryam]

Dear Alexey,

Thanks for your prompt response. Can I use ExaML to infer a tree on a set of RNA sequences? If so, which model should I use?

Thanks,
Mary

[Alexey Kozlov]

Hi Mary,

yes, please use DNA model for RNA sequences (-m DNA).

Best,
Alexey

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> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
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[Alexandros Stamatakis]

> Thanks for your prompt response. Can I use ExaML to infer a tree on a
> set of RNA sequences? If so, which model should I use?

Yes, you can, in terms of model selection you just proceed as for DNA
data. So GTRCAT or GTRGAMMA are a good choice here.

Alexis

>
> Thanks,
> Mary
>
>
>
>
> On Wednesday, August 22, 2018 at 12:24:15 PM UTC-7, Alexey Kozlov wrote:
>
> Hi Mary,
>
> if I recall it correctly ExaML parser supports PHYLIP alignments only.
>
> So could you please check and if necessary convert your alignment to
> PHYLIP (e.g. using the convertFasta2Phylip.sh
> script shipped with RAxML).
>
> Best,
> Alexey
>
> On 22.08.2018 20:58, Maryam wrote:
> > Hi,
> >
> > I have an alignment file which I used it to infer a tree using
> RAxMl and I did not get any error. Now I am going to use
> > ExaML on this alignment, but I keep getting this error: "problem
> reading number of species and sites". I should mention
> > that I do not have any space in the names of the specious.
> >
> > Thanks,
> > Mary
> >
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