Problem with

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Problem with

Hans Kraus

I have a problem with bulk loading a GFF into Chado. The error message
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/ line 3258, <$fh>
line 47993.

After a bit of debugging (by the way: the argument '--save_files'
doesn't exist, at least in my version of 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):
FN392320 GenBank gene 266 913 . - .
FN392320 GenBank mRNA 266 913 . - .
FN392320 GenBank CDS 266 913 . - .
FN392320 GenBank exon 266 913 . - . Parent=PAS_chr2-1_0002.t01

As usual: any help appreciated,

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