I got Mira to work but I had to increase, mmhr=3, I hope I didn't do anything wrong, although Bastien warn in manual about modifying mmhr. The problem is after Mira has finished I got a number of all contigs too high, All contigs=34276 contigs, and I think this number is too much for 250641 reads assembled, any clues about what is happening? Many thanks in advance and sorry for so many posts Juan El mié, 12-10-2011 a las 16:40 +0200, Juan Fernandez Tajes escribió: > Just for the record the reads were "cleaned" from vectors, adaptors, > polyA with seqtrimnext and cutadapt. > > This is the output message on the screen when mira stops due to the high > percentage of megahubs, although I know that bivalve is highly > repetitive in DNA sequences > > You have more than 0% of your reads found to be megahubs. > > You should sheck the following: > > 1) for Sanger sequences: are all the sequencing vectors masked / > clipped? > 2) for 454 sequences: are all the adaptors masked / clipped? > > You will find in the info directory a file called > '*_info_readrepeats.lst', > consult the MIRA manual on how to extract repeat information from there. > > *ONLY* when you are sure that no (or only a very negligible number) of > sequencing > vector / adaptor sequence is remaining, try this: > > 3) for organisms with complex repeats (eukaryots & some bacteria): > - reduce the -SK:nrr parameter (divide by 2) > 4) for EST projects, -SK:nrr will not really work, use -SK:nrr (start at > 10 and increase in steps of of 10) > > *ONLY* if the above fails, try increasing the -SK:mmhr parameter > Note that the number of present megahubs will increase computation time > in > an exponential way, so be careful when changing -SK:mmhr. > > > El mié, 12-10-2011 a las 16:14 +0200, Juan Fernandez Tajes escribió: > > Hi all, > > > > I have launched mira with -job=denovo,est,accurate,454 -highlyrepetitive > > -notraceinfo, nevertheless, mira stops and warns me about megahubs in my > > read (approximately a 2%). The program and the manual suggest set > > -SK:nrr set to 10, > > > > Do you think that with these parameters will fix the problem: > > > > -job=denovo,est,accurate,454 -highlyrepetitive -notraceinfo > > -SK:mnr=yes:nrr=10 > > > > > > Many thanks for the help > > > > Juan > > > > El jue, 06-10-2011 a las 00:04 +0200, Bastien Chevreux escribió: > > > On Monday 03 October 2011 23:47:58 Juan Fernandez Tajes wrote: > > > > > > > [...] > > > > > > > -job=denovo,est,accurate,454 -highlyrepetitive -notraceinfo, are > > > these > > > > > > > parameters appropriate?? > > > > > > > > > If you're not looking for something special, yes. > > > > > > > > > > It would be a better idea running a "draft", or "normal" assembly > > > before an > > > > > > > "accurate" one? > > > > > > > > > Not really. > > > > > > > > > B. > > > > > > > > > > > > -- 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