[maker-devel] augustus_species

[Gowthaman Ramasamy]

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/augustus%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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