[ensembl-dev] Biomart/martdb down?

[Premanand Achuthan]

Excellent tip. It works with -A. I have overlooked it.  Thanks Rhoda.

Regards
Prem

On 22/02/11 09:45, Rhoda Kinsella wrote:
> Hi Prem
> 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.
>
> mysql -uanonymous -hmartdb.ensembl.org -P5316 -A
>
> If there are issues in future with the www.biomart.org servers, you 
> can also access the Ensembl marts at 
> http://www.ensembl.org/biomart/martview
>
> I hope that helps,
> Regards
> Rhoda
>
>
> On 22 Feb 2011, at 09:12, Premanand Achuthan wrote:
>
>> Hi Steve
>>
>> Thanks for getting back. You are right, the biomart site is alright 
>> now. But still have issues with mysql server.
>>
>> xxx at xxx-vm:~$ mysql -uanonymous -hmartdb.ensembl.org -P5316
>> Welcome to the MySQL monitor.  Commands end with ; or \g.
>> Your MySQL connection id is 85312
>> Server version: 5.1.34 Source distribution
>>
>> Type 'help;' or '\h' for help. Type '\c' to clear the buffer.
>>
>> mysql> use vega_mart_61;
>> Reading table information for completion of table and column names
>> You can turn off this feature to get a quicker startup with -A
>>
>> Database changed
>> mysql> use ensembl_mart_61;
>> Reading table information for completion of table and column names
>> You can turn off this feature to get a quicker startup with -A
>>
>> ===
>> 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.
>>
>> Not sure if it has to do with my vms memory. Anyway, I can still go 
>> ahead with the biomart service.
>>
>> Thanks
>> Prem
>>
>>
>>
>>
>>
>>
>>
>> On 21/02/11 23:32, steve trevanion wrote:
>>> Hi Prem,
>>>
>>> Ensembl does not maintain the biomart website, please see 
>>> http://www.biomart.org/contact.html. However their site does now 
>>> appear to be OK
>>>
>>> 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 ?
>>>
>>> Regards,
>>>
>>> Steve
>>>
>>> On 21/02/2011 17:35, Premanand Achuthan wrote:
>>>> Hi All
>>>>
>>>> I have been trying to use biomart 
>>>> (http://www.biomart.org/biomart/martview/) since afternoon, and I 
>>>> keep getting the following message
>>>> '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'
>>>>
>>>> Also not able to connect to martdb.ensembl.org.ensembl_mart_61 
>>>> through mysql client.
>>>>
>>>> Anybody having similar issues?
>>>>
>>>> Thanks
>>>> Prem
>>>>
>>>>
>>>>
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>>>
>>>
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>>
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>
> Rhoda Kinsella Ph.D.
> Ensembl Bioinformatician,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
>

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