[Gmod-help] What is this?

[Scott Cain]

But, I think you should fix the CDS problems first: I'm not sure you
can trust the error message at the end of all those other errors.  The
"this shouldn't happen" message is indicative of a problem I didn't
consider, but that problem may be malformed GFF.  Fix that, and other
problems may go away.

Scott


On Wed, Sep 16, 2009 at 1:36 PM, Scott Cain <scott at scottcain.net> wrote:
> 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
>



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