[Bioperl-l] MSG when using Bio::DB::Taxonomy

Fields, Christopher J cjfields at illinois.edu
Fri Jul 11 11:57:13 UTC 2014

NCBI recently modified the URL for eutils, and it’s possible this wasn’t changed in the module.  I’ll try to have a look.


On Jul 10, 2014, at 11:21 PM, Cacau Centurion <cacaucenturion2 at gmail.com<mailto:cacaucenturion2 at gmail.com>> wrote:

Hi all,

I was told the following message when trying to use Bioperl.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't query website: 500 Can't connect to www.ncbi.nih.gov:80<http://www.ncbi.nih.gov/> (Bad hostname)
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
STACK: Bio::DB::Taxonomy::entrez::get_taxonids /usr/local/share/perl5/Bio/DB/Taxonomy/entrez.pm:472<http://entrez.pm:472/>

I use Bio::SearchIO and Bio::DB::Taxonomy in my script. It used to work properly but has met the problem recently. Does anyone know why?

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