[mira_talk] Re: Fishy tag

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.
>> 
> 
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