Have you tried with the FASTA file instead of the GBF one? J On 2011-02-16, at 4:03 PM, Louis Letourneau wrote: > I just tried 3.2.1.5 and got the same result. > The length is right there though, and I haven't manipulated the file in > any way. > ---> > Loading backbone from GBF file: staphAureus_backbone_in.gbf > > Fishy tag (to is greater than sequence length of 0): > ---> > > $ head staphAureus_backbone_in.gbf > LOCUS NC_007793 2872769 bp DNA circular BCT > 13-MAY-2010 > DEFINITION Staphylococcus aureus subsp. aureus USA300_FPR3757, complete > > > $ mira --version > This is MIRA V3.2.1.5 (development version). > > Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence > Assembly Using Trace Signals and Additional Sequence Information. > Computer Science and Biology: Proceedings of the German Conference on > Bioinformatics (GCB) 99, pp. 45-56. > > > > Is the length read from LOCUS line? > > Louis > > On 11-02-16 03:53 PM, Bastien Chevreux wrote: >> On Wednesday 16 February 2011 21:46:35 Bastien Chevreux wrote: >>> You have two options: >>> 1) try out a current development version of MIRA (3.2.1.5), where this bug >>> is fixed. For that, head to >>> http://sourceforge.net/projects/mira-assembler/files/MIRA/development/ >>> 2) convert the DOS format of the GenBank file to Unix format. I'd use >>> dos2unix or a number of other available tools for this. >>> http://kb.iu.edu/data/acux.html >>> gives a good overview >> >> On a second thought ... in case you have much more than 10m reads, going >> with >> 3.2.1.5 might be a better choice if you do not want to wait for too long for >> the assembly to finish. >> >> 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 -- 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