[Bioperl-l] Blastall problems

Simon Williams Simon.Williams at postgrad.manchester.ac.uk
Thu Mar 29 09:13:23 EDT 2007

Dear all,

I am having a few difficulties with standaloneblast. I am trying to implement a
web tool which will blast a given sequence before it goes on to do various
other things. I have a script to run the blast using the appropriate bioperl
modules which runs ok from the command line. The problem comes when I try to
run this through the web page. I get this output:

[blastall] FATAL ERROR: BlastFormattingInfoNew returned non-zero status
------------- EXCEPTION -------------
MSG: blastall call crashed: 256 /usr/bin/blastall -p blastp -d
"/fs/storage/data/db/blast/nr" -i /tmp/gldKFlbrJn -e 0.001 -o blast.out STACK
/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm:732 STACK
/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm:680 STACK
/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm:536 STACK toplevel

I'm not sure exactly what this means!
Any ideas would be gratefully received.


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