[Bioperl-l] Bio::Tools::Run::StandAloneBlastPlus - Illegal seek error running blastn

Mark A. Jensen maj at fortinbras.us
Thu Jan 28 10:56:14 EST 2010

Mike - please try updating your bioperl-live (the core) to the latest code 
(revision 16761 or so).
CommandExts is a work in progress; from the stack errors it looks like you've 
got an older version.
Try it then ping us back, if you would--
----- Original Message ----- 
From: "mike stubbington (BI)" <mike.stubbington at bbsrc.ac.uk>
To: <bioperl-l at lists.open-bio.org>
Sent: Thursday, January 28, 2010 10:41 AM
Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlastPlus - Illegal seek error 
running blastn

Dear all,

I am attempting to blast some primers against the mouse genome. I have created a 
local mouse genome blast database and I can search against it using 'blastn' at 
the command line.

I have perl code that creates an array of bioperl sequence objects called 

I then create a StandAloneBlastPlus factory using the following code…

my $blastFactory = Bio::Tools::Run::StandAloneBlastPlus->new(
-db_dir => '/Users/stubbing/localBlast/',
-db_name => 'MouseGenome'

and then attempt to blast my primers using this…

my @shortPrimers;
my $count=1;
foreach (@primers) {
my $currentSeq = $_;
print "Checking primer $count/$primerNumber ";
if ($_->length < 40) {
print "Too short!\n";
else {
print "BLASTing...";
my $blastResult = $blastFactory->blastn(-query => $currentSeq);

This fails with the following error…

------------- EXCEPTION -------------
MSG: /usr/local/ncbi/blast/bin/blastn call crashed: There was a problem running 
/usr/local/ncbi/blast/bin/blastn : Illegal seek at 
/Library/Perl/5.10.0/Bio/Tools/Run/WrapperBase/CommandExts.pm line 989, <DATA> 
line 532.

STACK Bio::Tools::Run::WrapperBase::_run 
STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD 
STACK Bio::Tools::Run::StandAloneBlastPlus::run 
STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD 
STACK toplevel ./5CTest.pl:63

Line 63 in my code is (as you might expect) the one that calls blastn on my 
factory object.

I'd appreciate any help you might be able to provide to shed light on this.

Thanks in advance,


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