Mmh... I still think the number of skims is fishy, but can't give further hypothesis if you say that the repeats are masked and reads are trimmed. I'm afraid you'll have to wait for Bastien's answer...
Just by curiosity, what pass is mira in? Has it gone through the first one at least?
L. On 14 Oct 2009, at 12:47 , Brian Forde wrote:
sorry yes it is still running. I am assuming that the data is highly repetitive but I have repeat masked it. The data is trimmed and includes a traceinfo fileOn Wed, Oct 14, 2009 at 11:44 AM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote: 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--"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
