[mira_talk] Re: Fishy tag

  • From: Louis Letourneau <louis.letourneau@xxxxxxxxxxxxxx>
  • To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
  • Date: Wed, 16 Feb 2011 16:03:06 -0500

I just tried 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
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?


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 (, 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 
> might be a better choice if you do not want to wait for too long for 
> the assembly to finish.
> B.

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