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

mike stubbington (BI) mike.stubbington at bbsrc.ac.uk
Fri Jan 29 08:25:25 EST 2010


Hi Mark,

Thanks for your continued help.

It now fails with this:

------------- EXCEPTION -------------
MSG: /usr/local/ncbi/blast/bin/blastn call crashed: There was a problem running /usr/local/ncbi/blast/bin/blastn : BLAST Database error: No alias or index file found for nucleotide database [MouseGenome] in search path [/Volumes/stubbing/PerlScripts/5CTest/trunk::]

STACK Bio::Tools::Run::WrapperBase::_run /Library/Perl/5.10.0/Bio/Tools/Run/WrapperBase/CommandExts.pm:1004
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
-------------------------------------

If I change the factory creation to:
my $blastFactory = Bio::Tools::Run::StandAloneBlastPlus->new(
	-db_name => '/Users/stubbing/localBlast/MouseGenome'
);

it fails with 

------------- EXCEPTION -------------
MSG: DB name not valid
STACK Bio::Tools::Run::StandAloneBlastPlus::new /Library/Perl/5.10.0/Bio/Tools/Run/StandAloneBlastPlus.pm:516
STACK toplevel ./5CTest.pl:45
-------------------------------------

However I can run the following successfully from the command line:

blastn -db  /Users/stubbing/localBlast/MouseGenome -query querySequence.fasta

Is there something wrong with how I'm referring to the blast database when I construct my factory?

Thanks again,

M



On 28 Jan 2010, at 18:47, Mark A. Jensen wrote:

> Hi Mike,
> Believe I found the real bug causing the problem (was not accounting for
> the db_dir parameter). Crashes should now also throw much more helpful
> errors. Please try the code at r16774, and shout back.
> thanks --
> MAJ
> ----- Original Message ----- 
> From: "mike stubbington (BI)" <mike.stubbington at bbsrc.ac.uk>
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Thursday, January 28, 2010 11:18 AM
> Subject: Re: [Bioperl-l] Bio::Tools::Run::StandAloneBlastPlus - Illegal seek 
> error running blastn
> 
> 
> 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
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> 
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