Question: I Use Blastdbcmd Command With Nr Database And It Gives Me The "Not Found Database" Error
gravatar for aliahmadvand2004
7.2 years ago by
aliahmadvand200450 wrote:

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?

blast • 5.6k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 7.2 years ago by aliahmadvand200450

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

ADD REPLYlink written 7.2 years ago by Istvan Albert ♦♦ 84k

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.

ADD REPLYlink written 7.2 years ago by Neilfws48k
gravatar for Andreas
7.2 years ago by
Andreas2.5k wrote:


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.


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

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Andreas2.5k
gravatar for vijay
7.2 years ago by
vijay1.5k wrote:

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.

ADD COMMENTlink written 7.2 years ago by vijay1.5k
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