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

Fri Jan 29 13:36:54 UTC 2010

Hi Mike-
Well, at least we're getting more informative errors. I think it's
still my bad; will look again. Both of your calls should work.
(thanks for the positive control too)
Thanks for your patience and the help--
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>; "Brian Osborne" <bosborne11 at verizon.net>
Sent: Friday, January 29, 2010 8:25 AM
Subject: Re: [Bioperl-l] Bio::Tools::Run::StandAloneBlastPlus - Illegal seek 
error running blastn

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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