Question: Error While Running Standalone Blast Via Bioperl
2
gravatar for vijay
6.0 years ago by
vijay1.4k
Chennai
vijay1.4k wrote:

Dear All,

I am trying to run a stand alone blast in my system. I have created a database locally and I am tying to run the blast against them using STANDALONEBLAST module of bioperl.

The code is as below.

#!C:/Perl64/bin/perl.exe -w

use strict;
use Bio::Tools::Run::StandAloneBlast;
use Bio::SearchIO;
use Bio::SeqIO;

my $in_file = "sample.fna";
my @params = (-p => 'blastn', -d => 'nt.12', -o => 'blast_report.fasta', -e     => '1e-5' );
my $seqio_object = Bio::SeqIO->new(-file => $in_file);
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);

When I execute the above script from my command line, it says

Replacement list is longer than search list at C:/Perl64/site/lib/Bio/Range.pm line 251

I am using Windows 7 64 bit with perl (v5.16.1) and Bioperl package 1.6.1.

Please can someone help me in fixing this error.

-vijay

bioperl blast • 1.9k views
ADD COMMENTlink modified 3.1 years ago by Biostar ♦♦ 20 • written 6.0 years ago by vijay1.4k

what's he origin of the blast database ? was it formated on your computer ?

ADD REPLYlink written 6.0 years ago by Pierre Lindenbaum112k

Why is it relevant? Isn't this a (incorrectly titled) question on how to use bioperl?

ADD REPLYlink written 6.0 years ago by Ketil3.9k

ah yes, sorry, I thought it was a problem with blast itself

ADD REPLYlink written 6.0 years ago by Pierre Lindenbaum112k
0
gravatar for Chris Fields
6.0 years ago by
Chris Fields1.9k
University of Illinois Urbana-Champaign
Chris Fields1.9k wrote:

This isn't an error as much as it is a general perl warning. The latest versions of BioPerl on CPAN have fixed this issue; have you tried that yet?

ADD COMMENTlink written 6.0 years ago by Chris Fields1.9k
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