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. Brian On 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"