[Bioclusters] BLAT users?

[Ran Rubinstein]

 I was asking because I am using BLAT with bigger databases (but smaller 
query load) on IRIX, with great success - but this could still affect me 
when the system goes into production. Is it an OSX specific issue? Were 
your problems solved?

Thanks,

David Adelson wrote:

> Thanks.  Stops working means no output generated for a considerable 
> time and 0%cpu usage for the process for some time.
>
> Jim Kent worked on this over the weekend and actually found 3 memory 
> leaks that he fixed.  The new source and binaries are available for 
> download from his website/ftpsite as v31.
>
> Dave Adelson
>
> On Nov 1, 2004, at 10:18 AM, Ran Rubinstein wrote:
>
>> Hi David
>>
>> Please elaborate on what does 'stop working' mean. The leaks program 
>> can find a lot more memory leaks and the program can still be correct 
>> - try looking at the process memory usage, and see if it grows over 
>> time, and whether it reaches the size of the physical RAM.
>>
>> Regards,
>>
>> David Adelson wrote:
>>
>>> This may be the wrong forum to look for an answer, but I thought I 
>>> would start here.
>>>
>>> We have been using BLAT on G4 Xserves (2GB RAM) for some time now.  
>>> Given the memory limitations, we carve up the database into chunks 
>>> so that we don't get a malloc error message telling us we have run 
>>> out of huge memory.  We then parallelize the job and run the chunks 
>>> in parallel on our cluster.  This works for modest query sizes 
>>> (15,000 ESTs vs 1.2GB database-hs_chroms1-6).  However, when we 
>>> scaled up to larger queries (493365 ESTs vs 1.3GB database-bovine 
>>> genome 200,000scaffolds) we see blat just sort of stop working after 
>>> a while.  I ran the leaks program and found 91832 memory leaks, so 
>>> the problem seems to be memory related.  I would be curious to know 
>>> if anyone else has seen this type of behavior with BLAT.  I am in 
>>> the process of contacting Jim Kent about this, but thought it would 
>>> not hurt to ask some other knowledgeable computational biologists 
>>> about this.
>>>
>>> thanks in advance,
>>>
>>> Dave Adelson
>>> Texas A&M University
>>>
>>> _______________________________________________
>>> Bioclusters maillist  -  Bioclusters@bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>>
>>>
>>
>>
>> -- 
>> Ran Rubinstein
>> Dept. of Molecular Biology
>> Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel
>> Tel +972-2-6757906 Fax +972-2-6758992
>>
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters@bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>
>


-- 
Ran Rubinstein
Dept. of Molecular Biology
Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel
Tel +972-2-6757906 Fax +972-2-6758992