error loading gff3 file to chado database
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17 months ago
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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:

this shouldn't happen in modified_uniquename at /Library/Perl/5.18/Bio/GMOD/DB/Adapter.pm line 3035, <GEN0> line 9249.
    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 please help me solve the issue?

chado gmod gff3 database • 399 views
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