[Gmod-help] Re: [Gmod-schema] Problems to Insert a Genbank in Chado

[Scott Cain]

Hi Fernando,

Those error messages are telling you that the conversion of your  
GenBank files into GFF3 did not go perfectly, since the types  
mature_peptide and pseudoCDS exist in the GenBank file, but do not  
exist in the Sequence Ontology, as required by the GFF3  
specification.  Because of the nature of GenBank records, it is very  
difficult to get the conversion of GenBank files to GFF3 perfect every  
time.

I suggest you replace the occurrences of mature_peptide with a SO term  
(the only one I can think of to replace it with is peptide, but there  
might be something better), and replace pseudoCDS with perhaps  
pseudogenic_exon.  (I'm not sure what the author means by pseudoCDS.   
Is it translated or not?)

You'll probably need to run your bulk load process with the -- 
recreate_cache option to clean up the mess left over from the previous  
failed load.

Scott


On Aug 26, 2009, at 1:57 PM, fernando bueno wrote:

> Hello
>
> I have downloaded from Ncbi genbanks of Triticum and used the script  
> bp_genbank2gff3.pl
> to convert this genbanks to Gff3.
> when a use the gmod_bulk_load_gff3.pl to insert this errors appears
>
>
> 1-
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no cvterm for mature_peptide
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/ 
> Root.pm:357
> STACK: Bio::GMOD::DB::Adapter::get_type /usr/local/share/perl/5.10.0/ 
> Bio/GMOD/DB/Adapter.pm:4224
> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:783
> -----------------------------------------------------------
> Issuing rollback() due to DESTROY without explicit disconnect() of  
> DBD::Pg::db handle dbname=chado;port=5432;host=localhost at /usr/ 
> local/share/perl/5.10.0/Error.pm line 184.
>
> 2-
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no cvterm for pseudoCDS
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/ 
> Root.pm:357
> STACK: Bio::GMOD::DB::Adapter::get_type /usr/local/share/perl/5.10.0/ 
> Bio/GMOD/DB/Adapter.pm:4224
> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:783
> -----------------------------------------------------------
> Issuing rollback() due to DESTROY without explicit disconnect() of  
> DBD::Pg::db handle dbname=chado;port=5432;host=localhost at /usr/ 
> local/share/perl/5.10.0/Error.pm line 184.
>
>
> I need your Help
> thank you!
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-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research