[Bioperl-l] [blastall] WARNING: Unable to open Batu.fa.nin

Manju Rawat manju.rawat2 at gmail.com
Wed Oct 12 01:32:06 EDT 2011


I am using the latest version of blast from
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/   for linux*.
* I created the database for Bos_taurus using Formatdb commamd of blast.

*agl at agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.txt -p F -o T*
database was create sucessfully and working properly in terminal..
but when i am using this database in bioperl programming it showing me balst
output with this warning that

[blastall] WARNING: Unable to open Batu.nin
[blastall] WARNING: Unable to open Batu.nin
[blastall] WARNING: Unable to open Batu.nin
[blastall] WARNING: Unable to open Batu.nin
[blastall] WARNING: Unable to open Batu.nin


and this is my program which i am running in terminal..

@params = ('database' => 'Btau','outfile' => 'bla.out',  '_READMETHOD' =>
'Blast', 'prog'=> 'blastn');

 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
 $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' );
 $input = $str->next_seq();
 $factory->blastall($input);


it working fine in terminal with following command but showing error in
programming..
agl at agl-desktop:~/BP$ blastall -p blastn -d btau -i test_query.fa -o
test.out

pl tell me what i am doing wrong.

Thanks
Manju Rawat


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