[mira_talk] Re: gff to gff3
- From: Felipe Lira <felipelira3@xxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 22 Oct 2014 16:47:55 +0000 (UTC)
That's my question.
In a simple view, there is no errors.
If I use this file that you put the link the output is the text that I
commented.
Felipe Lira
Spanish National Center of Biotechnology - CNB/ CSIC
Microbial Biotechnology DepartmentFellow of http://obrasocial.lacaixa.es/
Antes de imprimir este mensaje piense bien si es realmente necesario
hacerlo.Before you print this e-mail, think well if it is really necessary.
El Miércoles 22 de octubre de 2014 18:44, Peter Cock
<p.j.a.cock@xxxxxxxxxxxxxx> escribió:
No, I've not tried using MIRA convert for this, but don't the NCBI
provide quite nice GFF3 output nowadays?
i.e. What's wrong with this GFF3 file:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Stenotrophomonas_maltophilia_D457_uid162199/NC_017671.gff
Peter
On Wed, Oct 22, 2014 at 4:40 PM, Felipe Lira <felipelira3@xxxxxxxxxxxx> wrote:
> Anybody had tried to convert .gff file to .gff3 using miraconvert?
> It is what I have
>
> Fatal error (may be due to problems of the input data or parameters):
>
> *******************************************************************************
> * GFF file '../NC_017671.gff' had unrecoverable errors (see output above).
> *
> * Fix your file!
> *
> *
> *
> *******************************************************************************
>
> ->Thrown: void GFFParse::loadFile(const string & filename)
> ->Caught: main
>
> Aborting process, probably due to error in the input data or
> parametrisation.
> Please check the output log for more information.
> For help, please write a mail to the mira talk mailing list.
>
>
>
> Felipe Lira
> Spanish National Center of Biotechnology - CNB/ CSIC
> Microbial Biotechnology Department
> Fellow of http://obrasocial.lacaixa.es/
>
> Antes de imprimir este mensaje piense bien si es realmente necesario
> hacerlo.
> Before you print this e-mail, think well if it is really necessary.
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