[Gmod-help] What is this?

[Scott Cain]

Hi Fernando,

Is there a feature with an ID of WHTPH2AD in your GFF file or already
in your database?  Does it occur before any other line refers to it?

Scott


On Wed, Sep 16, 2009 at 1:28 PM, fernando bueno <stradlinbueno at gmail.com> wrote:
> Thanks for such a rapid answer!
>
> But... What about errors like unrecognized features, like the one at the
> bottom of the attached image file (unable to find source feature ...)
> The recreate_cache option isn't working...
>
> Thanks again...
>
> Fernando
>
> 2009/9/16 Scott Cain <scott at scottcain.net>
>>
>> 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
>>
>>
>>
>>
>
>



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