[ensembl-dev] DB connection and panic: sv_setpvn error

Anne Lyle annelyle at ebi.ac.uk
Tue May 27 09:31:48 BST 2014


On 26 May 2014, at 07:59, 陈岗 <danielchen06 at gmail.com> wrote:

> Hi All
> 
> Our mirror has database connection and sv_setpvn errors (version 75). The public-plugins/mirror/conf/ini-files/DEFAULTS.ini has been changed, but it doesn't work. The DB connection is not our real DB IP, user name and password.
> 

Did you remove config.packed after making changes to DEFAULTS.ini (e.g. using ctrl_scripts/restart_server -r)?


> And I have no idea for the second error, about panic: sv_setpvn.

Sorry, I have no idea either - hopefully someone from the Software (API) team will have insight into that one.

Cheers

Anne


> 
> The error massage:
> 
> First:
> 
>  Executing perl startup file
>  Retrieving conf from /usr/local/Ensembl/ensembl-webcode/conf/config.packed
> :: Auto-selecting build 546 core DB as:	anonymous at drosophila_melanogaster_core_75_546:ensembldb.ensembl.org:5306
> Could not connect to database drosophila_melanogaster_core_75_546 as user anonymous using [DBI:mysql:database=drosophila_melanogaster_core_75_546;host=ensembldb.ensembl.org;port=5306] as a locator:
> DBI connect('database=drosophila_melanogaster_core_75_546;host=ensembldb.ensembl.org;port=5306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (111) at /usr/local/Ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 262.
> Syntax error on line 152 of /usr/local/Ensembl/ensembl-webcode/conf/httpd.conf:
> 
> Second:
> 
> panic: sv_setpvn called with negative strlen -1 at /usr/local/Ensembl/ensembl/modules/Bio/EnsEMBL/Utils/Exception.pm line 420.\n
> 
> 
> Best regards
> 
> -- 
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, P.R.China
> Phone:(+86)512-82782588
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