Failing to run tblastn

1

Hello.

I'm trying to run tblastn and I get an error message. I'm posting the commands I gave and the error message I got, with hopes anyone would be able to provide some tips.

The commands:

export BLASTDB="/.../biodb/BLAST/Proteins2/nr"
module load blast/blast-2.10.0

Then I opened python and ran the following commands:

import subprocess

file = /path/to/fasta_file.fa
db_path="/.../biodb/BLAST/Proteins2/nr"
output_path="/output/path"

command = f'tblastn -query {file} -db {db_path} -max_hsps 1 -max_target_seqs 20 -num_threads 10 -evalue 1e-5' 
          f'-out {output_path + file[:-2]}txt -outfmt "6 qseqid sseqid pident staxids sskingdoms qstart qend ' 
          f'qlen length sstart send slen evalue mismatch gapopen bitscore stitle"'

subprocess.run(command, stdout=subprocess.PIPE, shell=True)

The error message:

BLAST Database error: No alias or index file found for nucleotide
database [/bioseq/biodb/BLAST/Proteins2/nr] in search path
[/powerapps/share/centos7/ncbi-blast/ncbi-blast-2.10.0+/blastdb:/bioseq/biodb/BLAST/Proteins2/nr:]

Thanks!


tblstn


blast

• 134 views

You're using a protein DB. you need a nucleotide one. which is usually named nt

the nt DB has this suffixes

nr.pal
nr.pdb
nr.pos
nr.pot
nr.ptf
nr.pto


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