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