[maker-devel] augustus_species

[Carson Holt]

The model files must go in .../augustus/config/species/ under the augustus
installation directory (Each model gets a different directory).  The
species that augustus can accept will be the same as the directory names
under .../augustus/config/species/. The command 'augustus --species=help'
will also provide a list of those names.

For the protein file can you send it to me?

--Carson


On 13-06-21 9:29 AM, "Gowthaman Ramasamy"
<gowthaman.ramasamy at seattlebiomed.org> wrote:

>I believe the model file should go to Augustus installation directory.
>Actually in to the 'genomes' sub folder there. Then use the exact name of
>the model file ( minus extension) in .CTL file.......
>
>"Bowen, Kara (De Leon)" <kara.deleon at biofilm.montana.edu> wrote:
>
>
>
>Hello,
>I am trying to annotation a Chlamydomonas genome and C. reinhartii was
>used as a model organism in Augustus.  I would like to add this model to
>augustus_species in the maker_opts.ctl file, but I'm not sure how this
>information should be inserted on this line (ie. as genus name, file
>location, etc).
>
>I am also having an issue with providing a protein file.  When I put in
>the protein fasta file of C. reinhartti from the Augustus website, I get
>a fatal error (below).  I've looked through the fasta and I'm not seeing
>anything obvious that would cause this error to be thrown.  Do you have
>any suggestions on where to start to look?
>
>
>Can't open sequence index file
>/Users/kara/Desktop/CBMW_maker_protein/contigs.maker.output/mpi_blastdb/au
>gustus%2Eu9_aa%2Efasta.mpi.10/augustus%2Eu9_aa%2Efasta.mpi.10.1.index:
>Inappropriate file type or format at /sw/lib/perl5/5.12.4/Bio/DB/Fasta.pm
>line 527.
>
>FATAL ERROR
>
>
>Thanks for any help you can provide.
>
>Kara
>
>
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>Kara De León
>Postdoctoral Research Associate
>Montana State University
>Center for Biofilm Engineering
>366 EPS Building
>Bozeman, MT 59717
>208-484-9078
>kara.deleon at biofilm.montana.edu<mailto:kara.deleon at biofilm.montana.edu>
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
>
>
>
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