[Bioperl-l] standalone blast won't work

Sendu Bala bix at sendu.me.uk
Mon Sep 4 06:28:40 EDT 2006


Carlo Lapid wrote:
> Hi,
> 
> I installed blast on my machine, and I wrote a test bioperl script that
> blasts a short test sequence against a small local database that I created.
> It worked fine. But when I incorporated the same code in a CGI script for a
> web-based program, I get the following error message in the error logs:

[...]
> /usr/local/blast-2.2.14/bin/blastall -p blastp  -d  /usr/local/blast-2.2.14/data/ig_heavy.gp  -i  /tmp/Cht6r7QkNs

Does a new CGI script that just runs the above command directly work? 
(you may need to change the input file and add an output file option to 
see if it works properly)

If it crashes as well this is a non-bioperl problem. Perhaps your server 
is set to kill high cpu/ long-running processes?


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