blastn execution error, the correct command line format

Question

[vigneshprbh37]

So I am trying to test my blast+ standalone program with the following command

./blastn -db /home/Desktop/ncbi-blast-2.2.30+/db/nr -query /home/Downloads/sequence.fasta -out /home/CCMB/Downloads/output/result

but every time I get the error not a valid output format

Can anyone give me an idea of the general execution command and format for nucleotide blast and correct me if my command is miswritten

I tried the command

./blastn -db /home/Desktop/ncbi-blast-2.2.30+/db/nr -query /home/CCMB/Downloads/sequence.fasta -out /home/Downloads/outbox/result.txt

but it always shows the error

BLAST Database error: No alias or index file found for nucleotide database [/home/Desktop/ncbi-blast-2.2.30+/db/nr] in search path [/home/Downloads/ncbi-blast-2.2.30+/bin::

Answer 1

[edrezen]

Hello,

You try to use blastn with the db bank being nr (protein bank), but blastn is made for comparing nucleotides bank vs another nucleotides bank.

So, you should use another db bank (like nt) or change to the correct blast tool (could be blastx in your case if your query bank has nucleotides)

Once your choice is made, you have to configure the db bank with the makeblastdb tool (look at this page). In your case, it should be something like this:

makeblastdb -in nr -dbtype prot

or

makeblastdb -in nt -dbtype nucl