[Bioperl-l] Blastall problems

Sendu Bala bix at sendu.me.uk
Thu Mar 29 14:06:51 UTC 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.



More information about the Bioperl-l mailing list