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

mike stubbington (BI) mike.stubbington at bbsrc.ac.uk
Thu Jan 28 11:18:12 EST 2010


Hi,

Thanks for the suggestion. Unfortunately it still fails - error as follows:

------------- 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 1000, <DATA> line 532.

STACK Bio::Tools::Run::WrapperBase::_run /Library/Perl/5.10.0/Bio/Tools/Run/WrapperBase/CommandExts.pm:1005
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
-------------------------------------

M

On 28 Jan 2010, at 15:56, Mark A. Jensen wrote:

> 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--
> Thanks
> Mark
> ----- 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 
> @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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> 
> 




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