On 23/06/09 6:27 PM, "David M. Goodstein" <[email protected]> wrote:
> We are wondering where the bottlenecks are in some of our simple queries (grab
> 30k peptides for a single organism into a fasta file) that take 10 minutes or
> more on an over-equipped under-utilized database server and web server.
>
>
Hi David,
You can turn the logging on (conf/ log4perl.conf), this will help you to
diagnose the problem.
A.
>
> David M. Goodstein
> Joint Genome Institute / Lawrence Berkeley National Lab
> Center for Integrative Genomics / UCBerkeley
> http://www.phytozome.net
>
>
>
>
> On 23 Jun 2009, at 15:22, Syed Haider wrote:
>
>> Hi David,
>>
>> biomart-perl/lib/BioMart/Initializer.pm
>>
>> look for INITBATCHSIZE
>>
>>
>> just wondering, why is that you want to change it ?
>>
>> Best,
>> Syed
>>
>>
>> David M. Goodstein wrote:
>>
>>> If I wanted query-runner to use a larger default initial_batchsize, where
>>> would I set that (e.g., conf/settings.conf), the MartRegistry xml, or
>>> somewhere else)?
>>> David M. Goodstein
>>> Joint Genome Institute / Lawrence Berkeley National Lab
>>> Center for Integrative Genomics / UCBerkeley
>>> http://www.phytozome.net
>>>
>
