Re: [Gusdev-gusdev] GBParser problems

[Jeetendra S. <so...@vb...>]

Hi Jinal,
     I had the same problem. After trying several files, I figured out
that the problem was the trailing spaces after the keyword ORIGIN.

     Try inserting few spaces after ORIGIN. It worked for me atleast. I
think I had mailed about this problem before, but didn't find any
better solution.

 --Jeetendra.


> I am trying to load a genbank file and the gbparser keeps giving me this
> message and finally goes out of memory and dies. Any idea what can be the
> problem? This genbank file was created by me from our newly sequenced
> genome
> and I am pretty sure that there is something missing in the format which
> the
> gbparser expects and that's why it dies. I validated my genbank file
> against
> "sequin" available from ncbi and everything looks good.
>
> Here is the message (the line "VLD     CBIL::Bio::GenBank::Origin      1"
> goes
> on and on)
>
> VLD     CBIL::Bio::GenBank::Features    1
> VLD     CBIL::Bio::GenBank::BaseCount   1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
> VLD     CBIL::Bio::GenBank::Origin      1
>
>
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-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu