Hi Betina, Another simple thing that comes to mind is to "vacuum full analyze" (assuming you are using postgres). This seems to greatly improve Apollo load times for me.
You could also try performance tuning your db server: http://wiki.postgresql.org/wiki/Tuning_Your_PostgreSQL_Server http://www.revsys.com/writings/postgresql-performance.html assuming you have more resources, memory to give. I've managed to get my load times down slightly this way. HTH, -j On Thu, Sep 24, 2009 at 10:33 PM, Ed Lee <[email protected]> wrote: > Hi Betina, > > If you're fetching 454 reads, it doesn't surprise me that it is rather > slow, since you'll have a lot of read to fetch. This is probably due > to the highly normalized nature of Chado. I'd imagine that anything > that is reading off the database directly and fetching so many > results (which causes a large number of joins to be made) will be > slow. Perhaps you could look into using materialized views, which > I believe the most current release of Chado supports. However, > Apollo's code would have to be updated to support these views. > > Cheers, > Ed > > On Thu, 24 Sep 2009, Betina Porcel wrote: > >> Hi there! >> Today, I'm have some doubts concerning Apollo's performance. >> Here my problem: >> still using Apollo1.10.0 connected to a Chado DB >> >> I've been testing the time Apollo needs to open a genomic region, and here >> the result: >> >> when trying on a region with no much stuff (some repeats and abInitio >> results, always on the results side), Apollo is taking more less 30 seconds >> to open a 5kb region. But! when trying on a region where all the resources >> are present (results of proteins alignements, ESTs, and mostly 454 reads!) >> opening 10kb is taking me 5 minutes. >> >> I know that the more results you have in the database, the longer the >> time Apollo takers to open your genomic region, is the performance I'm >> getting "normal"? What about your experiences? >> We'll be starting a manual curation projet soon, and I'm pretty worried >> about the time that'll take for our colleaugues to open Apollo!!!! >> >> >> Any suggesstions? >> >> >> Thanks a lot!!!! >> >> Betina >> >> _______________________________________________ >> apollo mailing list >> [email protected] >> http://mail.fruitfly.org/mailman/listinfo/apollo >> >> > _______________________________________________ > apollo mailing list > [email protected] > http://mail.fruitfly.org/mailman/listinfo/apollo > -- ________________ http://five.sentenc.es/ _______________________________________________ apollo mailing list [email protected] http://mail.fruitfly.org/mailman/listinfo/apollo
