[Bioperl-l] Blastall problems

Sendu Bala bix at sendu.me.uk
Thu Mar 29 10:06:51 EDT 2007


Simon Williams wrote:
> 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
> Bio::Tools::Run::StandAloneBlast::_runblast
> /usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm:732 STACK
> Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> /usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm:680 STACK
> Bio::Tools::Run::StandAloneBlast::blastall
> /usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm:536 STACK toplevel
> /fs/storage/home/williams/public_html/crescendo_cgi/pdb_extra/blastSeqGetter.pl:33
> --------------------------------------
> 
> I'm not sure exactly what this means!

As the message says, the blastall call crashed. Perhaps your http user 
doesn't have permission to run blastall or access the necessary files.


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