[ensembl-dev] Can't connect Ensembl Database-The server is down

[enrico1970 at yahoo.com]

The server for the version 48 upwards looks like down. 

The server ensembldb.ensembl.org on port 5306, that allows connection to the ensembl 48 onwards (http://www.ensembl.org/info/data/mysql.html) looks like down. I cannot connect to that server while I can connect to the port 3306:

mysql  -u anonymous  -P 5306 -h ensembldb.ensembl.org

ERROR 2003 (HY000): Can't connect to MySQL server on 'ensembldb.ensembl.org' (111)



mysql  -u anonymous  -P 3306 -h ensembldb.ensembl.org
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 36672 to server version: 4.1.20-standard-log

I executed Jiang's code using the version with 46 and it works (while it did not work with version 67):

use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
      -host       =>'ensembldb.ensembl.org',
      -user       =>'anonymous',
      -db_version =>'46');

Best regards,

Enrico





________________________________
 From: JiangMei <gingerplum at hotmail.com>
To: dev at ensembl.org 
Sent: Saturday, 27 October 2012, 6:33
Subject: [ensembl-dev] Can't connect Ensembl Database
 

 
Hi All. Sorry to bother you.

I can't connect the Ensembl database.

My code is as following
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
      -host       =>'ensembldb.ensembl.org',
      -user       =>'anonymous',
      -db_version =>'67');
my @adaptors=@{$registry->get_all_adaptors(-GROUP => 'core', -TYPE => 'gene')};

open IN,"IDs.txt";
while(<IN>){
      chomp;
      my ($gene,$name,$species);
      $id=$_;
      for $adaptor(@adaptors){
       $gene=$adaptor->fetch_by_stable_id($id);
       }
      $name=$gene->external_name;
      $species=$gene->species;
}
close IN;

Then I got the following error:
MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:5306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org' (111)
STACK Bio::EnsEMBL::Registry::load_registry_from_db /root/Ensembl-67/ensembl/modules/Bio/EnsEMBL/Registry.pm:1576

Is there anything wrong with my code? Wish your help! Thanks very much! I really appreciate it.


Best regards,

Mei


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