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Excellent tip. It works with -A. I have overlooked it. Thanks
Rhoda.<br>
<br>
Regards<br>
Prem<br>
<br>
On 22/02/11 09:45, Rhoda Kinsella wrote:
<blockquote
cite="mid:DB4D1F97-ADF7-4F47-A016-24B53C6A0979@ebi.ac.uk"
type="cite">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 <a class="moz-txt-link-abbreviated" href="http://www.biomart.org">www.biomart.org</a>
servers, you can also access the Ensembl marts at <a
moz-do-not-send="true"
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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</blockquote>
<pre wrap=""><fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
Dev mailing list
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</pre>
</blockquote>
<br>
</div>
_______________________________________________<br>
Dev mailing list<br>
<a moz-do-not-send="true" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
<a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><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-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;">
<div style="word-wrap: break-word;"><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;">
<div style="word-wrap: break-word;">
<div>Rhoda Kinsella Ph.D.</div>
<div>
<div style="margin: 0px; font: 12px 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>
</blockquote>
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