Error while loading gff file

[shmenolin]

I used the following command to load annotations from a gff file to chado database:

gmod_bulk_load_gff3.pl --organism <organism name in db> --gfffile <gff_file.gff.sorted> --remove_lock

The file runs but creates the following error for every CDS feature it processes:

	Bio::GMOD::DB::Adapter::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x7fc1c9fb3ca0)', 'orig_id', undef, 'organism_id', 2) called at /Library/Perl/5.18/Bio/GMOD/DB/Adapter.pm line 3995
	Bio::GMOD::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x7fc1c9fb3ca0)', 'Bio::SeqFeature::Annotated=HASH(0x7fc1ca171978)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 824

There is a CDS feature with no parent (ID:fig|6666666.574109.peg.998)  I think that is wrong!

Then it terminates as soon as it reaches a RNA feature in the annotation file, raising the following error:

Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Loading data into dbxref table ...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Loading data into featureloc table ...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
DBD::Pg::db pg_endcopy failed: ERROR:  invalid input syntax for type bigint: ""
CONTEXT:  COPY feature_synonym, line 1, column pub_id: "" at /Library/Perl/5.18/Bio/GMOD/DB/Adapter.pm line 3263, <$fh> line 9304.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: calling endcopy for feature_synonym failed: 
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.18/Bio/Root/Root.pm:449
STACK: Bio::GMOD::DB::Adapter::copy_from_stdin /Library/Perl/5.18/Bio/GMOD/DB/Adapter.pm:3263
STACK: Bio::GMOD::DB::Adapter::load_data /Library/Perl/5.18/Bio/GMOD/DB/Adapter.pm:3185
STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:1076
-----------------------------------------------------------

Abnormal termination, trying to clean up...

Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...
Must call pg_endcopy before issuing more commands at /Library/Perl/5.18/Bio/GMOD/DB/Adapter.pm line 1438, <$fh> line 9304.

Could you help me solve the issue?

[scottcain]

oof, sorry this is so old and I haven't responded to it. Apparently I need to do a better job letting github notifications surface.

Anyway, the first message about There is a CDS feature with no parent is because, while you can have CDS features with no parent in legal GFF, the Chado loader expects them to be present as part of a "central dogma" gene (ie, gene->mRNA->exon,CDS) or at least with a transcript as a parent (mRNA->CDS). The loader is warning that the data may not be saved the way you'd want it to be (although to be fair, since it has been a very long time since I've touched this code, I can't remember exactly what it would do).

As for the synonym/feature_synonym problem, I would want to see some entries from the GFF that have Alias attributes in them to see if I could figure out what is going wrong with them. I can't tell from this message if it is a bug in the (pretty old) perl code, or in the GFF that you're trying to load.