Sounds strange indeed... Should have completed by now. I'm not completely familiar with the gears of mira, but it seems to me that you have a huge amount of skims (hits, if I'm correct) for your number of reads... do you have highly repeated data? Non-trimmed data?
And by the way, is the mira process still alive? Lionel On 14 Oct 2009, at 10:52 , Brian Forde wrote:
Hi lionel,I have approx only 550,000 reads. Its a 454 project only. I am assuming that it has stalled as memory usage is down to 1%. From what you are saying it appears to me that some thing has gone wrong.BrianOn Wed, Oct 14, 2009 at 9:45 AM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote:Hi Brian,What pass are you in? (grep "Pass" assembly_log.txt) How many reads do you have (looks like an awful lot)? Is the process terminated (ps -A | grep mira)?My guess is that you have a zillion reads and mira is still sorting reads. It has loaded 2.7 Giga-skims (elements), so that might take some time to sort... in my genome, I have 3 M reads and I get about 34 Mega-skims, i.e. 100 times less...Hope that helps Lionel On 14 Oct 2009, at 10:25 , Brian Forde wrote:I havebeen running a mapping assemblu of a geome for a few days now but it appears to be hanging. I checked it yesteday evening and again this morning and it hasn't moved. I was wondering if it was hanging and if i can quit (losing the assembly in the process).the last entry in the log is De-normalising SKIM hits ... (this will take a while) Loading skims in id range 0 to 213398 Loaded 2 773 837 688 elements. Sorting ... --"If scientists knew what they were doing they wouldn't call it research"--You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html--"If scientists knew what they were doing they wouldn't call it research"
============================================ Lionel Guy Thunmansgatan 25, SE-75421 Uppsala phone: +46 (0)18 245596 mobile: +46 (0)73 9760618 email: guy.lionel@xxxxxxxxx ============================================ -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html
