<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Prem<div>When you are connecting to the marts it is advisable to use -A as the Ensembl marts are quite large. This option skips auto hashing and allows faster access to the tables. </div><div><br></div><div>mysql -uanonymous -hmartdb.ensembl.org -P5316 -A</div><div><br></div><div>If there are issues in future with the www.biomart.org servers, you can also access the Ensembl marts at <a href="http://www.ensembl.org/biomart/martview">http://www.ensembl.org/biomart/martview</a></div><div><br></div><div>I hope that helps,</div><div>Regards</div><div>Rhoda</div><div><br></div><div><br><div><div>On 22 Feb 2011, at 09:12, Premanand Achuthan wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div text="#000000" bgcolor="#ffffff"> Hi Steve<br> <br> Thanks for getting back. You are right, the biomart site is alright now. But still have issues with mysql server.<br> <br> xxx@xxx-vm:~$ mysql -uanonymous -hmartdb.ensembl.org -P5316<br> Welcome to the MySQL monitor. Commands end with ; or \g.<br> Your MySQL connection id is 85312<br> Server version: 5.1.34 Source distribution<br> <br> Type 'help;' or '\h' for help. Type '\c' to clear the buffer.<br> <br> mysql> use vega_mart_61;<br> Reading table information for completion of table and column names<br> You can turn off this feature to get a quicker startup with -A<br> <br> Database changed<br> mysql> use ensembl_mart_61;<br> Reading table information for completion of table and column names<br> You can turn off this feature to get a quicker startup with -A<br> <br> ===<br> I have waited here for more than 10 minutes, still it doesn't switch. vega_mart_61 seems to be fine, but not able to use ensembl_mart_61.<br> <br> Not sure if it has to do with my vms memory. Anyway, I can still go ahead with the biomart service.<br> <br> Thanks<br> Prem<br> <br> <br> <br> <br> <br> <br> <br> On 21/02/11 23:32, steve trevanion wrote: <blockquote cite="mid:4D62F5F8.8080206@sanger.ac.uk" type="cite"> Hi Prem,<br> <br> Ensembl does not maintain the biomart website, please see <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.biomart.org/contact.html">http://www.biomart.org/contact.html</a>. However their site does now appear to be OK<br> <br> We do maintain martdb.ensembl.org and that is responding fine for me. We have not had any other reports of problems, can you confirm you are using port 5316 ?<br> <br> Regards,<br> <br> Steve<br> <br> On 21/02/2011 17:35, Premanand Achuthan wrote: <blockquote cite="mid:4D62A259.2000003@cimr.cam.ac.uk" type="cite"> Hi All<br> <br> I have been trying to use biomart (<a moz-do-not-send="true" href="http://www.biomart.org/biomart/martview/">http://www.biomart.org/biomart/martview/</a>) since afternoon, and I keep getting the following message <br> '<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: medium;"><span class="Apple-style-span" style="font-family: sans-serif;">Serious Error: Could not connect to mysql database ensembl_mart_61: DBI connect('database=ensembl_mart_61;host=dcc-qa-db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to MySQL server on 'dcc-qa-db.oicr.on.ca' (113) at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98'<br> <br> Also not able to connect to </span></span>martdb.ensembl.org.ensembl_mart_61 through mysql client.<br> <br> Anybody having similar issues?<br> <br> Thanks<br> Prem<br> <br> <br> <pre wrap=""><fieldset class="mimeAttachmentHeader"></fieldset>
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</pre> </blockquote> <br> </div> _______________________________________________<br>Dev mailing list<br><a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>http://lists.ensembl.org/mailman/listinfo/dev<br></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Rhoda Kinsella Ph.D.</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Ensembl Bioinformatician,</div></div><div>European Bioinformatics Institute (EMBL-EBI),<br>Wellcome Trust Genome Campus, </div><div>Hinxton<br>Cambridge CB10 1SD,</div><div>UK.</div></div></span></div></span> </div><br></div></body></html>