Re: [BioMart Users] [Reactome-help] Fwd: [Ensembl #243847] Error DataMart Reactome Pathway - www.ensembl.org

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Re: [BioMart Users] [Reactome-help] Fwd: [Ensembl #243847] Error DataMart Reactome Pathway - www.ensembl.org

David Croft
Hi Bert,

Things look fine when I access the mart directly from the Reactome web
site, but you are right, it isn't working properly when you access it
from the ENSEMBL web site.  Odd!  Perhaps somebody on the Mart users
list knows what's going on?

Cheers,

David.

> The Reactome BVioMart instance that is accessed through Ensembl (so
> from http://www.ensembl.org/biomart/martview/) still gives an error
> message when one wants to export results:
>
> Pathway stable ID Pathway DB_ID
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
> Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table './test_reactome_mart/pathway__pathway__main' was
> created with a different version of MySQL and cannot be read
>
> Cheers,
> Bert
> On Mon, Dec 5, 2011 at 10:31 AM, David Croft<[hidden email]>  wrote:
>> Hi Bert,
>>
>>> The Reactome BioMart that can be accessed from the Ensembl site gives
>>> the error mentioned below. The BioMart that can be accessed from the
>>> Reactome site itself seems to work fine. Do these two BioMarts run
>>> from different databases? If so, who is responsible for the first one?
>>>
>>>
>> As Robin said, we have been having hardware problems recently, sorry for the
>> inconvenience!  Could you check the Reactome BioMart server again?  It
>> should now be working normally, though perhaps a little slowly.
>>
>> Cheers,
>>
>> David.
>>
>>
>>> ---------- Forwarded message ----------
>>> From: alejandro fernandez via RT<[hidden email]>
>>> Date: Fri, Dec 2, 2011 at 2:49 PM
>>> Subject: [Ensembl #243847] Error DataMart Reactome Pathway -
>>> www.ensembl.org
>>> To:
>>>
>>>
>>>
>>> Fri Dec 02 14:49:13 2011: Request 243847 was acted upon.
>>> Transaction: Ticket created by [hidden email]
>>>        Queue: ensembl-helpdesk
>>>      Subject: Error DataMart Reactome Pathway - www.ensembl.org
>>>        Owner: Nobody
>>>   Requestors: [hidden email]
>>>       Status: new
>>>   Ticket<URL: https://rt.sanger.ac.uk/Ticket/Display.html?id=243847>
>>>
>>>
>>> Support question from www.ensembl.org
>>>
>>> Date:            2011-12-02 14:49:12
>>> Name:            Alejandro Fernandez
>>> Referer:         http://www.ensembl.org
>>> Last Search:     -none-
>>> User agent:      Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.1
>>> (KHTML, like Gecko) Ubuntu/11.10 Chromium/14.0.835.202
>>> Chrome/14.0.835.202 Safari/535.1
>>>
>>> Comments:
>>>
>>> When I try to download the Reactome pathway I get the following error:
>>>
>>>
>>> sv____html;HTML,txt;TXT,tsv;TSV,xls;XLS____tsv____html;HTML,txt;TXT,tsv;TSV,xls;XLS____
>>> Pathway stable ID       Pathway DB_ID
>>> Query ERROR: caught BioMart::Exception::Database: Error during query
>>> execution: Table './test_reactome_mart/pathway__pathway__main' was
>>> created with a different version of MySQL and cannot be read
>>> Query ERROR: caught BioMart::Exception::Database: Error during query
>>> execution: Table './test_reactome_mart/pathway__pathway__main' was
>>> created with a different version of MySQL and cannot be read
>>> Query ERROR: caught BioMart::Exception::Database: Error during query
>>> execution: Table './test_reactome_mart/pathway__pathway__main' was
>>> created with a different version of MySQL and cannot be read
>>> Query ERROR: caught BioMart::Exception::Database: Error during query
>>> execution: Table './test_reactome_mart/pathway__pathway__main' was
>>> created with a different version of MySQL and cannot be read
>>> Query ERROR: caught BioMart::Exception::Database: Error during query
>>> execution: Table './test_reactome_mart/pathway__pathway__main' was
>>> created with a different version of MySQL and cannot be read
>>> Query ERROR: caught BioMart::Exception::Database: Error during query
>>> execution: Table './test_reactome_mart/pathway__pathway__main' was
>>> created with a different version of MySQL and cannot be read
>>> Query ERROR: caught BioMart::Exception::Database: Error during query
>>> execution: Table './test_reactome_mart/pathway__pathway__main' was
>>> created with a different version of MySQL and cannot be read
>>> Query ERROR: caught BioMart::Exception::Database: Error during query
>>> execution: Table './test_reactome_mart/pathway__pathway__main' was
>>> created with a different version of MySQL and cannot be read
>>> Query ERROR: caug
>>>
>>>
>>>
>>>
>>>
>>> --
>>>   The Wellcome Trust Sanger Institute is operated by Genome Research
>>>   Limited, a charity registered in England with number 1021457 and a
>>>   company registered in England with number 2742969, whose registered
>>>   office is 215 Euston Road, London, NW1 2BE.
>>>
>>>
>
>

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