you just need to run the consensus option with the sequential or
pthreads version of raxml, the MPI version does not support this,
alexis
On 26.12.2015 21:21, Juan C. Opazo wrote:
> Dear Alex, I have the following question, I ran the bootstrap analysis
> and when I am tried to get the consensus tree using the this command:
>
> mpirun -n 2 raxmlHPC-MPI -m PROTGAMMAJTT -J MR -z
> RAxML_bootstrap.outfile -n con
>
> I got this message:
>
> *This is RAxML MPI Process Number: 0
> Error: you are running the parallel MPI program but only want to compute
> one tree
> For the MPI version you must specify a number of trees greater than 1
> with the -# or -N option
>
> This is RAxML MPI Process Number: 1
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
> --------------------------------------------------------------------------*
>
> I tried changing the -n to 1, but I got the same message, also if I
> remove the first portion of the command ( mpirun -n 2).
>
> Do you have any idea of what is going on?
>
> thank you in advance
>
> Juan
>
> On Wed, Dec 9, 2015 at 3:51 AM, Juan C. Opazo <
jop...@gmail.com
> <mailto:
jop...@gmail.com>> wrote:
>
> you are right, the names are similar, but anyways, thank you to both
> of you for helping me with my questions.
>
> best
>
> juan
>
> On Wed, Dec 9, 2015 at 6:56 AM, Alexandros Stamatakis
> <
alexandros...@gmail.com
> Note that Alexey also answered on here (he is my PhD student) so
> it was not only me who helped, I admit the names are pretty similar.
>
> Alexey, I've noted that I need to include a check for #processes < 2
>
> raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> and I got the model, nothing else.
>
> After including the "mpirun -n 2"as you suggested:
>
> mpirun -n 2 raxmlHPC-MPI -s Alignment.fasta -p 12345 -m
> PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> I am also obtaining the best tree. Is that ok? the best tree
> reconstruction is using the best model selected?
>
>
> That should be the case, but I am not 100% sure if this is what
> the code does, I will need to check, but it will take some time
> until I get to this.
>
> Alexis
>
>
> best
>
> juan
>
>
> On Tue, Dec 8, 2015 at 9:45 PM, Juan C. Opazo
> <
jop...@gmail.com <mailto:
jop...@gmail.com>
> <mailto:
raxml%25252Bun...@googlegroups.com
> <mailto:
raxml%2525252Bu...@googlegroups.com>
>
> <mailto:
raxml%2525252Bu...@googlegroups.com
> <mailto:
raxml%252525252B...@googlegroups.com>>>>>
> <mailto:
raxml%25252Bun...@googlegroups.com
> <mailto:
raxml%2525252Bu...@googlegroups.com>
>
> <mailto:
raxml%2525252Bu...@googlegroups.com
> <mailto:
raxml%252525252B...@googlegroups.com>>>>>>.
> <mailto:
raxml%25252Bun...@googlegroups.com
> <mailto:
raxml%2525252Bu...@googlegroups.com>
>
> <mailto:
raxml%2525252Bu...@googlegroups.com
> <mailto:
raxml%252525252B...@googlegroups.com>>>>>.
> For more options, visit
>
https://groups.google.com/d/optout.
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs.
> Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>>
> <tel:56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674
> <tel:56-63-2221674>>>
> <tel:56-63-2221674 <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>> <tel:56-63-2221674
> <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>>>>
> fax: 56-63-2221344
> <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>
> <tel:56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221344 <tel:56-63-2221344>>> <tel:56-63-2221344
> <tel:56-63-2221674 <tel:56-63-2221674>>> <tel:56-63-2221674
> <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>>
> <tel:56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674
> <tel:56-63-2221674>>>>
> fax: 56-63-2221344
> <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>
> <tel:56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221344 <tel:56-63-2221344>>> <tel:56-63-2221344
> <tel:56-63-2221344>
> <tel:56-63-2221344 <tel:56-63-2221344>>
> <tel:56-63-2221344 <tel:56-63-2221344> <tel:56-63-2221344
> <tel:56-63-2221344>>>>
> jopazo (at) gmail (dot) com
>
> OpazoLab <
http://www.opazolab.cl/>
> ResearchGate
> <
https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención
> Ecología y
> Evolución <
http://www.ecolevol.cl>
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> <tel:56-63-2221674> <tel:56-63-2221674 <tel:56-63-2221674>>
> 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>
>