[Gmod-schema] [ISSUE] Load gff in chado

[RAJAONISON A. <mir...@ya...>]

Hi, 

 

Hi, 

Hope this mail will find you well. Send you my best wishes for this new
year. 

I am reaching to you because I have issues loading GFF files into you Chado.
I tried several files but none of them seems to work.

 

Thank you in advance for you help 

 

Miharimamy

 

1.	The S.cerevisiae example in gmod.org

Command : 

chado-1.31/load/bin/gmod_bulk_load_gff3.pl --organism yeast --gfffile
saccharomyces/saccharomyces_cerevisiae.gff.sorted --fastafile
saccharomyces/saccharomyces_cerevisiae.gff.sorted.fasta

 

Output : 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: Error in line:

chrIII  SGD     chromosome      1       316620  .       .       .
ID=chrIII;dbxref=NCBI:;Name=chrIII

 

Dbxref value 'NCBI:' did not conform to GFF3 specification

STACK: Error::throw

STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:447

STACK: Bio::FeatureIO::gff::_handle_feature
/usr/local/share/perl5/Bio/FeatureIO/gff.pm:659

STACK: Bio::FeatureIO::gff::next_feature
/usr/local/share/perl5/Bio/FeatureIO/gff.pm:187

STACK: chado-1.31/load/bin/gmod_bulk_load_gff3.pl:782

-----------------------------------------------------------

2.	S.cerevisiae without dbxref

Command : 

chado-1.31/load/bin/gmod_bulk_load_gff3.pl --organism yeast --gfffile
saccharomyces/test_saccharomyces_ncbi --fastafile
saccharomyces/saccharomyces_cerevisiae.gff.sorted.fasta

 

Output : 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: I couldn't find the 'Note' cvterm in the database;

Did you load the feature property controlled vocabulary?

STACK: Error::throw

STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:447

STACK: Bio::GMOD::DB::Adapter::handle_note
/usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm:3901

STACK: chado-1.31/load/bin/gmod_bulk_load_gff3.pl:974

 

3.	A GFF from NCBI

Command : 

chado-1.31/load/bin/gmod_bulk_load_gff3.pl --organism bacteria --gfffile
GCF_000008865.2/GCF_003018035.1_ASM301803v1_genomic.gff.sorted

 

Output :

Unable to find srcfeature NZ_CP027390.1 in the database.

Perhaps you need to rerun your data load with the '--recreate_cache' option.
at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4605, <GEN0> line 2.

 
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x241
a8d0)', 'Bio::SeqFeature::Annotated=HASH(0x26c61d0)') called at
chado-1.31/load/bin/gmod_bulk_load_gff3.pl line 851

 

4.	A GFF3 from prokka

Command :

chado-1.31/load/bin/gmod_bulk_load_gff3.pl --organism bacteria -gfffile
GFF3/GCF_000455285.gff.sorted --fastafile
GFF3/GCF_000455285.gff.sorted.fasta

Output :

Unable to find srcfeature gnl|Prokka|GCF_000455285_1 in the database.

Perhaps you need to rerun your data load with the '--recreate_cache' option.
at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4605, <GEN0> line 2.

 
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x330
08f0)', 'Bio::SeqFeature::Annotated=HASH(0x35ac0a0)') called at
chado-1.31/load/bin/gmod_bulk_load_gff3.pl line 851