Hi Titus, I think the .seqDict uses large memory because you have 16m sequence IDs. Are you using AnnotDB for your NLMSA? I remember that you used dummy object to save annotation object? In that case, I think pygr would use greater memory. That is all I can think of...
Yours, Namshin Kim On Thu, Jun 25, 2009 at 11:26 PM, C. Titus Brown <[email protected]> wrote: > > Hi folks, > > I'm building an NLMSA with about 16m alignments at the moment, and > memory consumption has risen to 15gb. The process is *only* building > the NLMSA (using my bowtie-to-nlmsa script) so it's not from anywhere > else. Is this expected behavior, or could there be memory leaks etc? > > thanks, > --titus > -- > C. Titus Brown, [email protected] > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
