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

mike stubbington (BI) mike.stubbington at bbsrc.ac.uk
Thu Jan 28 10:41:49 EST 2010


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 @primers

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 ($_->length < 40) {
			push(@shortPrimers,$_);
			print "Too short!\n";
		}
		else {
			print "BLASTing...";
			my $blastResult = $blastFactory->blastn(-query => $currentSeq);
		}
		$count++;
	}

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 /Library/Perl/5.10.0/Bio/Tools/Run/WrapperBase/CommandExts.pm:994
STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:1236
STACK Bio::Tools::Run::StandAloneBlastPlus::run /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm:267
STACK Bio::Tools::Run::StandAloneBlastPlus::AUTOLOAD /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:1233
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,

Mike





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