[Bioperl-l] blast module errors with web app

Samantha Thompson Samantha.Thompson at greenbiologics.com
Tue Dec 9 14:34:56 EST 2008



I seem to be able to get stand alone blast to run ok, using a script
like the one in the Beginner's HowTo ... 

But when running it embedded in my web app I get the following


------------- EXCEPTION: Bio::Root::Exception -------------

MSG: blastall call crashed: -1 /usr/bin/blastall -d  "/src/GBLCCDB16s"
-i  /tmp/FxXS98W1H0  -o  /tmp/6gp_EnCnsu  -p  blastn 


STACK: Error::throw

STACK: Bio::Root::Root::throw

STACK: Bio::Tools::Run::StandAloneBlast::_runblast

STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast

STACK: Bio::Tools::Run::StandAloneBlast::blastall


This comes from the stack trace of my Catalyst web app....

I wonder if these particular exceptions mean anything to anyone. Does
BLAST not like the database have folder names in it? Maybe theres a
problem with the tmp folder not existing as part of my web app. Maybe I
need to explicitly define the -i and -o parameters...





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