Hi Jan, I had a similar problem myself, and changing the default value for option -AS:bdq solved it. I think mira sets the default base quality value to 10 for sanger reads, and the clipping quality to 20 (option -CL:qcmq). This is probably why none of your sequences are kept. So if you set option -AS:qcmq to less 10 or option -AS:bdq to more than 20, your reads should be used, and mira will keep rolling ! e.g., if you trust your genbank sequences you can even increase a buit more their default quality : SANGER_SETTINGS -AS:bdq=40 Regards Jorge. --- Jorge Duarte Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Z.I. Du Brézet 8, Rue des Frères Lumière 63028 CLERMONT FERRAND Cedex 2 FRANCE Tel : +33 (0)4 73 39 60 73 Fax : +33 (0)4 73 39 60 71 E-mail : jorge.duarte@xxxxxxxxxxxx mira_talk-bounce@xxxxxxxxxxxxx a écrit sur 02/04/2009 09:19:24 : > Hi Bastien and all, > > I assembled bacterial genome (~7M, 30 coverage on 454 not paired). Today > I just for curiosity added fasta files from that particular bug which > are already known from genbank (~200 short records, marginal part of the > genome, not suitable for mapping), but without success. It looks I have > problem with reading sanger fasta files, but I can't figure out, how to > overcome it. > > Details follows: > > Shortly after starting mira: > > mira -project=mira_v3 -job=denovo,genome,sanger,454,accurate > COMMON_SETTINGS -GE:not=8 > > i got: > > <code> > Short length: FS4OOG301DEWUX (454): only 39 good bases, need: 40. No > paired end partner, rejected. > Short length: FS4OOG301BF1EN (454): only 38 good bases, need: 40. No > paired end partner, rejected. > Short length: FS4OOG301C692T (454): only 38 good bases, need: 40. No > paired end partner, rejected. > Short length: FS4OOG301CAS2J (454): only 38 good bases, need: 40. No > paired end partner, rejected. > Short length: ^C > [1]+ Floating point exception > </code> > > however, reading fasta files seems to work fine: > > <code> > Loading data normal (probably Sanger type) from FASTA files, > Counting sequences in FASTA file: > Loading sequence data from FASTA file mira_v3_in.sanger.fasta: > Could not find FASTA quality file mira_v3_in.sanger.fasta.qual, using > default qualities for all reads. > Done. > Loaded 207 reads, 0 of which have quality accounted for. > </code> > > but clipping went wrong for all sanger reads: > > <code> > Short length: a001 (san): only 0 good bases, need: 80. No paired end > partner, rejected. > </code> > > Thanks for any suggestions, > > Jan > > -- > 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