I Use Blastdbcmd Command With Nr Database And It Gives Me The "Not Found Database" Error

Question

[aliahmadvand2004]

This is the error

BLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/home/aj3/Desktop/h/database::]

what should I do? do I have to use any other commands prior to this one to make the database ready or what?

[Istvan Albert]

also please don't ask two identical questions, the other has been deleted

[Neilfws]

It did not give you the "not found database" error: the error is "No alias or index file found" - as you state yourself.

Difficult to diagnose the issue without more information, but one possibility is that you have the wrong database. "nr" usually refers to non-redundant protein, but your error refers to a nucleotide database.

Answer 1

[Andreas]

Hi,

can you see an index file in /home/aj3/Desktop/h/database? It's a file with the extension "nal" (for nucleotides). If it's missing, you possibly forgot to run a makeblastdb (previously formatdb) on your fasta file.

Andreas

PS: providing the full command line you used and a listing of your database directory would help a lot

Answer 2

[vijay]

As rightly pointed out by Andreas, the index file for your nr database might have gone missing. Create an index file using makeblastdb as suggested. Also, do check on the folder location from which you run the blast executable. Usually all the database files shall be placed under blast-2.2.27+\db folder . Blast would look for the index file automatically in this folder. Alternatively you can run the blast directly from the location where you have your db files.

Hope this helps.