[ensembl-dev] Region report tool / Registry - only works for mysql users without password?

Kieron Taylor ktaylor at ebi.ac.uk
Mon Apr 30 16:28:20 BST 2012

Hi Nick, I'm glad to see someone is using the Region report tool from 
the command line.

There is a bug that we know of in the secondary host connection code, 
which is being fixed, but there are a couple of things we have noticed 
in your parameter specification.

Firstly, pointing the tool at the same server twice redundant. The 
feature is in place to assist in situations (such as on our main public 
servers) where data must be spread across several hosts. Hopefully you 
are just masking your true connection settings.

Secondly, MySQL behaves badly with "localhost" as a target. It tends to 
assume socket connections instead of by http, which can cause no end of 
connection issues. Sockets are treated differently for valid users and 
authentication than through HTTP. Try feeding it as a host 


On 30/04/12 16:00, Nick Langridge wrote:
> Hi,
> I'm trying to use the region report tool but it seems to ignore the
> mysql password that I supply in the options:
> perl region_report.pl --species=Anopheles_gambiae --input=/tmp/inputfile
> --include=gt --report --host=localhost --port=3306 --db_version=66
> --user=myuser --password=mypass --secondaryhost=localhost
> --secondaryport=3306 --db_version=66 --secondaryuser=myuser
> --secondarypassword=mypass --output=/tmp/outputfile
> I see error:
> connect: DBI:mysql:host=localhost;port=3306 myuser at
> /ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm
> line 1566.
> DBI connect('host=localhost;port=3306','myuser',...) failed: Access
> denied for user 'myuser'@'localhost' (using password: NO) at
> /ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm
> line 1567
> -------------------- EXCEPTION --------------------
> MSG: Cannot connect to the Ensembl MySQL server at localhost:3306; check
> your settings & DBI error message: Access denied for user
> 'myuser'@'localhost' (using password: NO)
> STACK Bio::EnsEMBL::Registry::load_registry_from_db
> /ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm:1567
> STACK Bio::EnsEMBL::Registry::load_registry_from_multiple_dbs
> /ensembl/www-live/VB-2012-03/ensembl/modules/Bio/EnsEMBL/Registry.pm:2296
> STACK toplevel
> /ensembl/www-live/VB-2012-03/ensembl-tools/scripts/region_reporter/region_report.pl:176
> Ensembl API version = 66
> ---------------------------------------------------
> As far as I can see, the region report script calls
> Bio::Ensembl::Registry->load_registry_from_multiple_dbs() with the
> password present, but the registry seems to ignore it.
> Is this the expected behaviour?
> Cheers,
> Nick
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