[Bioperl-l] Error with supplied lineages importing uniprot data

Sendu Bala bix at sendu.me.uk
Fri Dec 1 04:03:13 EST 2006


pelikan at cs.pitt.edu wrote:
> Hello all,
> 
>  I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows,
> without Cygwin. The "make test"s have all completed without error. This
> is my first time dealing with bioperl, so bear with me.
> 
>    I've successfully loaded the most recent taxonomy information using the
> biosql-schema scripts. After this, I attempted to load the most recent
> release of the uniprot flat file dataset with the following command:
> 
> load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass
> ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat
> 
> I am subsequently greeted by many of the following errors:
> 
> Could not store Q7N3Q6:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: The supplied lineage does not start near 'Photorhabdus luminescens
> subsp. laumondii'

In your uniprot_sprot.dat file there'll be some kind of entry with that 
Photorhabdus species. Can you post that entry (sans sequence if it has 
one) so I can take a look at it? Maybe post a few that cause problems, 
and a few that don't.


More information about the Bioperl-l mailing list