I'm setting up a gbrowse2 server, and I noticed the queries to the apache2 server all end up in
Timeout waiting for output from CGI script /var/www/cgi-bin/gb2/gbrowse
Here I'm dealing with hundreds of thousands of sequences (40GB of eukaryotic genome annotation), therefore I guess the database needs to be indexed. I'm using MySQL. Question is: which table/field should be indexed? I couldn't find an answer on their tutorial.
Thanks a lot!
EDIT: yes, the demo examples work. Also my data, reduced to less than 10GB of GFF3 lines, is working perfectly with no timeout. Addittionally, increasing the timeout limits in the gbrowse.conf file will eventually provide a result. I tried the speed-up tricks suggested by the gbrowse tutorial (i.e. increasing the memory available for MySQL), without a big improvement in the performance. I know there is a field in a table of the gbrowse2 database that needs to be indexed to have a massive improvement in the performance. I thought that would be feature::seqid or name::name but no success.