[BioBrew Users] BLAST db > 2 GB

[Glen Otero]

You've run into a 32-bit Linux file size limit that BioBrew can't 
change. You should be able to format your nt db into volumes 
(fromatdb's -v flag if I remember correctly) to get around this 
limitation. Using mpiBLAST to break up the db is also an option. What 
version of BioBrew are you using? I might have to point you to the new 
mpiBLAST packages.

Glen

On Apr 1, 2004, at 12:07 PM, Chris Beck wrote:

> Caveat: still a complete newb, please forgive my ignorance - I tried 
> to find similar problems but I am not doubt looking in the wrong 
> place. RTFM replies are welcome, if they include a link to TFM :)
>
> We're experiencing a problem where our BLAST nt db is > 2 GB and this 
> causing problems for our linux STDIN/STDOUT.
> Does this problem exist in Biobrew?  If it does, can biobrew work 
> around it by splitting up the db and recombining the results?
>
> Cheers,
> Chris
> -- 
> Chris Beck / Y.A.B.A. / Fungal Genomics / CFSG / Concordia University
> Chaos.  Panic.  Confusion.  My work here is done.
>
> _______________________________________________
> BioBrew-Users mailing list
> BioBrew-Users at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>
>
Glen Otero, Ph.D.
Linux Prophet
619.917.1772