Hi TItus, Strange. I re-installed & tested several times and it is same as before. Still, it took seconds to load all hash table and uses memory. As you said, I used the screed from acraker github.
Thanks! Namshin Kim On Thu, May 14, 2009 at 10:54 PM, C. Titus Brown <c...@msu.edu> wrote: > > On Thu, May 14, 2009 at 05:31:58PM +0900, Namshin Kim wrote: > -> One quick question. > -> When I tried to open ScreedSequenceDB, there is an initial delay, a few > -> seconds. It seems screed is trying to load all hash tables into memory > (I > -> checked the memory and it *is* using large memory). Is there any way to > -> avoid large memory usage? > > Hi Namshin, > > you are correct, and Alex tells me that the latest version has fixed all > of that (I asked him to consider use cases with 1 bn sequences in a > FASTQ file ;). I will be taking a look at it over the weekend, but it > should all be working & the Python interface is backwards compatible. > You can get it here, > > http://github.com/acracker/screed/tree/master > > Let me know what you think. > > --titus > -- > C. Titus Brown, c...@msu.edu > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
