[Gmod-help] What is this?

[Scott Cain]

Hello Fernando,

The conversion of GenBank files to GFF3 sometimes doesn't work  
perfectly, and presumably that is what happened here.  You will  
probably need to edit the file to fix it.

About the warning messages, the first most obvious explanation is that  
there are CDS features that are not part of a gene or mRNA, and the  
loader thinks "that is wrong!"  :-)  Additionally, I see that you got  
the message about gamma-gliadin twice.  While it is valid GFF3 for  
fragments of a CDS feature to share an ID to group them together, the  
bulk loader does not support that.  In order to group two or more  
pieces of a CDS together, they must have a common parent, like a gene  
or preferably an mRNA.

If it isn't obvious what you need to fix, you can send a sample of the  
GFF and we can take a look and make suggestions.  Also, I suggest in  
the future that if you have problems with Chado that you send email to  
the schema mailing list:

   https://lists.sourceforge.net/lists/listinfo/gmod-schema

Scott


On Sep 14, 2009, at 4:57 PM, fernando bueno wrote:

> Hi,
>
> I'm using  gmod_bulk_load_gff3,pl to insert a genbank on my chado  
> database. The following messages pop up all time, and I don't know  
> if the data is correctlly inserted.
> Is there something you can do to help me with this issue?
>
> Thanks,
>
> Fernado
>
>
>
>
> There is a CDS feature with no parent (ID:gamma-gliadin)  I think  
> that is wrong!
>
> this shouldn't happen in modified_uniquename at /usr/local/share/ 
> perl/5.10.0/Bio/GMOD/DB/Adapter.pm line 2647
>      
> Bio 
> ::GMOD 
> ::DB 
> ::Adapter 
> ::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x9938910)',  
> 'orig_id', undef) called at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/ 
> Adapter.pm line 3604
>      
> Bio 
> ::GMOD 
> ::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x9938910)',  
> 'Bio::SeqFeature::Annotated=HASH(0xaf275e8)') called at /usr/local/ 
> bin/gmod_bulk_load_gff3.pl line 756
>
>
> There is a CDS feature with no parent (ID:gamma-gliadin)  I think  
> that is wrong!
>
> this shouldn't happen in modified_uniquename at /usr/local/share/ 
> perl/5.10.0/Bio/GMOD/DB/Adapter.pm line 2647
>      
> Bio 
> ::GMOD 
> ::DB 
> ::Adapter 
> ::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x9938910)',  
> 'orig_id', undef) called at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/ 
> Adapter.pm line 3604
>      
> Bio 
> ::GMOD 
> ::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x9938910)',  
> 'Bio::SeqFeature::Annotated=HASH(0xaf4aa60)') called at /usr/local/ 
> bin/gmod_bulk_load_gff3.pl line 756
>
>
> There is a CDS feature with no parent (ID:cystatin)  I think that is  
> wrong!
>
> this shouldn't happen in modified_uniquename at /usr/local/share/ 
> perl/5.10.0/Bio/GMOD/DB/Adapter.pm line 2647
>      
> Bio 
> ::GMOD 
> ::DB 
> ::Adapter 
> ::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x9938910)',  
> 'orig_id', undef) called at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/ 
> Adapter.pm line 3604
>      
> Bio 
> ::GMOD 
> ::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x9938910)',  
> 'Bio::SeqFeature::Annotated=HASH(0xaf7f338)') called at /usr/local/ 
> bin/gmod_bulk_load_gff3.pl line 756
>
>
> There is a CDS feature with no parent (ID:HPPK/DHPS)  I think that  
> is wrong!
>
> this shouldn't happen in modified_uniquename at /usr/local/share/ 
> perl/5.10.0/Bio/GMOD/DB/Adapter.pm line 2647
>      
> Bio 
> ::GMOD 
> ::DB 
> ::Adapter 
> ::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x9938910)',  
> 'orig_id', undef) called at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/ 
> Adapter.pm line 3604
>      
> Bio 
> ::GMOD 
> ::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x9938910)',  
> 'Bio::SeqFeature::Annotated=HASH(0xaf8c528)') called at /usr/local/ 
> bin/gmod_bulk_load_gff3.pl line 756
>
>

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research