<html><body><div style="color:#000; background-color:#fff; font-family:Courier New, courier, monaco, monospace, sans-serif;font-size:14pt">The server for the version 48 upwards looks like down. <br><br>The server <span>ensembldb.ensembl.org on port 5306, that allows connection to the </span>ensembl <strong>48</strong> 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:<br><span><br></span>mysql -u anonymous -P 5306 -h ensembldb.ensembl.org<br><div><span>ERROR 2003 (HY000): Can't connect to MySQL server on 'ensembldb.ensembl.org' (111)<br></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span><br></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif;
background-color: transparent; font-style: normal;"><span><br></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>mysql -u anonymous -P 3306 -h ensembldb.ensembl.org<br>Welcome to the MySQL monitor. Commands end with ; or \g.<br>Your MySQL connection id is 36672 to server version: 4.1.20-standard-log</span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br><span></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span>I executed Jiang's code using the version with 46 and it works (while it did not work with version 67):</span></div><div
style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span><br></span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;">use Bio::EnsEMBL::Registry;<br>my $registry = 'Bio::EnsEMBL::Registry';<br>$registry->load_registry_from_db(<br> -host =>'ensembldb.ensembl.org',<br> -user =>'anonymous',<br> -db_version =>'46');</div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px;
font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;">Best regards,</div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;">Enrico<br><span> </span></div><div style="color: rgb(0, 0, 0); font-size: 18.6667px; font-family: Courier New,courier,monaco,monospace,sans-serif; background-color: transparent; font-style: normal;"><span><br></span></div><div><span></span></div><div><br></div> <div style="font-family: Courier New, courier, monaco, monospace, sans-serif; font-size: 14pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial"
size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> JiangMei <gingerplum@hotmail.com><br> <b><span style="font-weight: bold;">To:</span></b> dev@ensembl.org <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday, 27 October 2012, 6:33<br> <b><span style="font-weight: bold;">Subject:</span></b> [ensembl-dev] Can't connect Ensembl Database<br> </font> </div> <br><meta http-equiv="x-dns-prefetch-control" content="off"><div id="yiv1528880931">
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Hi All. Sorry to bother you.<br><br>I can't connect the Ensembl database.<br><br>My code is as following<br>use Bio::EnsEMBL::Registry;<br>my $registry = 'Bio::EnsEMBL::Registry';<br>$registry->load_registry_from_db(<br> -host =>'ensembldb.ensembl.org',<br> -user =>'anonymous',<br> -db_version =>'67');<br>my @adaptors=@{$registry->get_all_adaptors(-GROUP => 'core', -TYPE => 'gene')};<br><br>open IN,"IDs.txt";<br>while(<IN>){<br> chomp;<br> my ($gene,$name,$species);<br> $id=$_;<br> for $adaptor(@adaptors){<br> $gene=$adaptor->fetch_by_stable_id($id);<br>
}<br> $name=$gene->external_name;<br> $species=$gene->species;<br>}<br>close IN;<br><br>Then I got the following error:<br>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)<br>STACK Bio::EnsEMBL::Registry::load_registry_from_db /root/Ensembl-67/ensembl/modules/Bio/EnsEMBL/Registry.pm:1576<br><br>Is there anything wrong with my code? Wish your help! Thanks very much! I really appreciate it.<br><br><br>Best regards,<br><br>Mei<br><br> </div></div>
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