Smithies, Russell | 13 Jan 23:25 2013
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Re: stand alone blast plus problem

Hi Frej,
Here's a few things to try:
Is it possible you need to escape the special chars in your IDs? i.e. the pipes and colons?
Have you tried it with simpler IDs?
Is your BioPerl sequence object collection created correctly?
Can you create the database by just passing it the fasta file?

$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
  -db_name => 'mydb',
  -db_data => 'myseqs.fas',
  -create => 1
);

--Russell 

-----Original Message-----
From: bioperl-l-bounces <at> lists.open-bio.org [mailto:bioperl-l-bounces <at> lists.open-bio.org] On
Behalf Of Frej Tulin
Sent: Friday, 11 January 2013 3:53 p.m.
To: bioperl-l <at> bioperl.org
Subject: [Bioperl-l] stand alone blast plus problem

Hi

I have been trying for a long time to control my blast searches with the
Bio::Tools::Run::StandAloneBlastPlus module.

The module is installed and gets loaded ok.

However, when calling:
my $blast_db = Bio::Tools::Run::StandAloneBlastPlus -> new
(    -db_data => \ <at> seq_arr,
    -create => 1);

$blast_db -> make_db();
----------------------------------------------------------------------
I get this error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb call crashed: There was a problem running
/home/frej/ncbi-blast-2.2.27+/bin/makeblastdb : Error:
NCBI C++ Exception:

"/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp",
line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type
ATCG00500.1

STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/frej/perl5/lib/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run
/home/frej/perl5/lib/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
STACK: Bio::Tools::Run::StandAloneBlastPlus::make_db
/home/frej/perl5/lib/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm:776
STACK: comp2fasta.pl:57
-------------------------------------------------------------------------------------------------------------------------------

The general header format of the fasta files I've tried are
>ATCG00500.1|PACid:19637947
or
>g8540.t1|PACid:26887931

I always get the same message.
I have tried modifying the header by putting 'lcl|' in from but nothing seems to help.
When I build a database using the makeblastdb directly from the command line it works ok, it just doesn't
work from within bioperl.

How can this be? What am I doing wrong?

helpful for any assistance

best
/frej

--
Frej Tulin
Fred Cross lab
Rockefeller University
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