[Bioperl-l] bioseqDB error

snoze pa snoze.pa at gmail.com
Wed Jan 30 12:34:24 EST 2008


Hilmar,

The command I am using is following

load_seqdatabase.pl -host localhost -namespace bioperl -dbname bioseqdb
-dbuser root -format genbank sequences.txt

I have no idea why i am getting that error

thanks in advance


On Jan 29, 2008 3:40 PM, Hilmar Lapp <hlapp at gmx.net> wrote:

> This would mean that two or more seqfeatures with the same type for
> the same sequence exist in the input data, each with rank 1.
>
> Normally the rank will be incremented for each seqfeature of a
> sequence, so I'm not sure how this is happening here w/o seeing the
> data.
>
>        -hilmar
> On Jan 29, 2008, at 12:15 PM, snoze pa wrote:
>
> > Dear Users,
> > I tried the to refresh installation and seems it is working. But
> > when I
> > loading sequences then it is giving me following warning messages.
> > Am i
> > doing alright? or i am missing huge chunk of sequences..Thanks in
> > advance
> > s
> >
> > -------------------- WARNING ---------------------
> > MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
> > values
> > were ("","1") FKs (27,3,4)
> > Duplicate entry '27-3-4-1' for key 2
> > ---------------------------------------------------
> > ...
> > ...
> > and so on
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
>


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