Problem with gmod_bulk_load_gff3.pl

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Problem with gmod_bulk_load_gff3.pl

Hans Kraus
Hi,

I have a problem with bulk loading a GFF into Chado. The error message
is:
--------------------------------START---------------------------------
Loading data into feature_relationship table ...
DBD::Pg::db pg_endcopy failed: FEHLER:  ungültige Eingabesyntax für
ganze Zahl: »«
KONTEXT:  COPY feature_relationship, Zeile 21043, Spalte type_id: »«
at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3258, <$fh>
line 47993.
---------------------------------END----------------------------------

After a bit of debugging (by the way: the argument '--save_files'
doesn't exist, at least in my version of gmod_bulk_load_gff3.pl) I found
the following:

About 21,000 features are (as I suppose) automatically generated. They
are all from two different types:
1) exon-auto<feature_id> (about 11,000)
2) polypeptide-auto<feature_id> (about 10,100)

The exon ones are processed without fault. But all entries in the
featureloc file for the polypeptide ones are missing the value for
the type_id.

The entries in the GFF look OK for me (one as example):
--------------------------------START---------------------------------
FN392320 GenBank gene 266 913 . - .
ID=PAS_chr2-1_0002;locus_tag=PAS_chr2-1_0002
FN392320 GenBank mRNA 266 913 . - .
ID=PAS_chr2-1_0002.t01;Parent=PAS_chr2-1_0002
FN392320 GenBank CDS 266 913 . - .
ID=PAS_chr2-1_0002.p01;Parent=PAS_chr2-1_0002.t01;Dbxref=GI:238030678,UniProtKB/TrEMBL:C4QZC7;codon_start=1;locus_tag=PAS_chr2-1_0002;product=Hypothetical
protein;protein_id=CAY68601.1;translation=length.215
FN392320 GenBank exon 266 913 . - . Parent=PAS_chr2-1_0002.t01
.
.
.
 >PAS_chr2-1_0002.p01
MMASPTAGDHPAGDGPASGAQLGGEAGGATGEVSQVFQVRASASASPGGTVLEVEVSRED
---------------------------------END----------------------------------

As usual: any help appreciated,
Hans

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