On Friday 07 October 2011 00:01:56 jyotsna guleria wrote: > I tried what you suggested still it didn't work.. :( > > Here is the new logfile with changes: > > http://dl.dropbox.com/u/10010521/logfile Interesting. MIRA actually assembles almost all your reads in previous passes into a single contig with ~6k reads and a length of ~450bp. That is not really behaving like a normal genome, you know :-) A routine kicks in which is there to try and find reads which spoil an assembly ... and it marks a lot of these reads as spoil sports. Try this: -AS:sd=no Bastien