[Gmod-help] Gbrowse GFF Flybase

[Fabian Schmich]

Dear Help Desk,

we're trying to set up a gbrowse server to use for internal lab 
annotation on drosophila melanogaster. I downloaded the current release 
(r5.23) from flybase 
[ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.23_FB2009_10/gff/] 
and removed the 'target' tag in the 'orthologous_to' features as 
recommended in the README. After that, I created a mysql database 
'dmel523' and started to load the chromosomes into the database, with 
the command: 'bp_seqfeature_load.pl -u XXX -p XXX -d dmel523 -c -f 
dmel-2L-r5.23.gff dmel-2R-r5.23.gff dmel-3L-r5.23.gff dmel-3R-r5.23.gff 
dmel-4-r5.23.gff dmel-X-r5.23.gff'. As for the config file in the 
gbrowse.conf, I copied and adjusted the recommended 09.fly.conf file, 
that comes with gbrowse.

When I try to browse the chromosomes on the web frontend of gbrowse 
after the data was loaded, I experience problems with chromosome X and 
4. Whenever I try to access chromsome X, for instance, by searching the 
landmark 'X', I don't get the usual 'Overview' and 'Details' section, 
but a message stating 'The following 1 regions match your request' 
followed by the line 'X:1..22422827     Bio::DB::SeqFeature::Segment    
 X:1 bp..22.42 Mbp (22.42 Mbp)     score=n/a'. Similar problems occur 
with chromosome 4. The other chromosomes (2L, 2R, 3L, 3R) are ok and 
working as expected.

The only time chromsome 4 (or X) seem to work, is when I load the 
database with only chromosome 4 (or X). As soon as I upload another 
chromosome the same error occurs. I also tried release 4.3 and it worked 
without any issues, but we do want to run release 5.x.

Do you have any ideas on what's wrong here? Am I missing some 
preprocessing steps? I'd appreciate any hint!


Best Wishes,

--
Fabian Schmich