Question: Warning Unable To Open .Nin
0
gravatar for Manju
7.5 years ago by
Manju0
Manju0 wrote:

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@agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.fa -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.fa.nin
[blastall] WARNING: Unable to open Batu.fa.nin
[blastall] WARNING: Unable to open Batu.fa.nin
[blastall] WARNING: Unable to open Batu.fa.nin
[blastall] WARNING: Unable to open Batu.fa.nin

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

@params = ('database' => 'Btau.fa','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);

pl tell me what i am doing wrong.

Thanks Manju Rawat

bioperl blast • 3.3k views
ADD COMMENTlink modified 7.5 years ago by Eric Fournier1.4k • written 7.5 years ago by Manju0
1
gravatar for Kieren Lythgow
7.5 years ago by
Southampton
Kieren Lythgow110 wrote:

Hi,

I think you need to alter your formatdb command as -i is supposed to be the FASTA sequences that your database will consist of. You have not specified the name of your actual database. Try the following command

formatdb -p F -i Btau.fa -n BtauDB -o T

ADD COMMENTlink written 7.5 years ago by Kieren Lythgow110
1

Also your error message from blastall refers to 'Batu.fa.nin'.....

ADD REPLYlink written 7.5 years ago by Kieren Lythgow110
1

I think the above observation is the key :)

ADD REPLYlink written 7.5 years ago by Neilfws48k
1
gravatar for Eric Fournier
7.5 years ago by
Eric Fournier1.4k
Quebec, Canada
Eric Fournier1.4k wrote:

Your error says "Unable to open Batu.fa.nin". Your perl excerpt has "Btau.fa, though. The issue might simply be caused by a typo.

ADD COMMENTlink written 7.5 years ago by Eric Fournier1.4k

Sharp eyes! I missed that!

ADD REPLYlink written 7.5 years ago by Daniel3.7k

I did point this out yesterday...

ADD REPLYlink written 7.5 years ago by Kieren Lythgow110

Then what should i write in databse....my database name is btau...and i have 7 files of database..i.e btau.nin,btau.nni....etc...

ADD REPLYlink written 7.5 years ago by Manju50
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