[mira_talk] Re: gff to gff3
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 22 Oct 2014 18:00:32 +0100
Hi Felipe,
Could you also show us the mira convert command you ran
(the email title says converting gff to gff3, which does not make
sense if you already have a gff3 file), and which version of
MIRA you are using.
Also, was there anything else in the output you have left out
which might explain what the fatal error was?
Peter
On Wed, Oct 22, 2014 at 5:47 PM, Felipe Lira <felipelira3@xxxxxxxxxxxx> wrote:
> 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 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.
>
>
> 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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