no alias or index file found for nucleotide database nr in search path error

Question

[AyehSadr]

Dear All

I have downloaded the nr database by this command wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz' and have extracted the files. When I run blastx I got this error: no alias or index file found for nucleotide database nr in search path.

I would appreciate to guide me how I can fix it.

Best Regards Ayeh

[Joe]

Please post the command you used to invoke blastx.

My guess would be you didn’t use the basename for the database nr (you shouldn’t provide any extensions).

It might also be helpful to show a snippet of the directory listing after you extracted the archive.

[AyehSadr]

the command is:

blastx -query '/home/fatemeh/trinity_outp/Trinity.fasta' -db '/home/fatemeh/NCBI/nr' -out blastx.outfmt6 -evalue 1e-4 -num_threads 4 -max_target_seqs 1 -outfmt 6

[Joe]

There shouldn’t be any need to put your filepaths in quotation marks, but I doubt this is the cause of your issue.

Please show us some of the content of the directory. ls -l | head -n 20 should suffice (unless you have a lot of non-Blast related stuff in the same directory).

[AyehSadr]

ls -l | head -n 20
total 452
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 28 11:19 nr.00
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 12:34 nr.01
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 12:40 nr.02
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 12:40 nr.03
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 12:41 nr.04
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 12:43 nr.05
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 14:55 nr.06
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 14:55 nr.07
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 14:55 nr.08
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 14:56 nr.09
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 14:57 nr.10
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 15:56 nr.100
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 15:57 nr.101
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 15:57 nr.102
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 15:58 nr.103
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 15:58 nr.104
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 15:59 nr.105
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 15:59 nr.106
drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 16:00 nr.107

[Joe]

Can you also tell us how you extracted the files? I would suggest using the update_blastdb.pl script NCBI provides for downloading all the parts. As your initial error suggested, you're missing a number of parts for the database to work properly

For instance, if I download nr.00.tar.gz only as an example:

$ tar xvzf nr.00.tar.gz
nr.pal
nr.00.pin
nr.00.phr
nr.00.psq
nr.00.pni
nr.00.pnd
nr.00.psi
nr.00.psd
nr.00.ppi
nr.00.ppd
nr.00.phi
nr.00.phd
nr.00.pog
taxdb.btd
taxdb.bti

You are missing all of these files at the moment. I'm not convinced everything has extracted properly. What size were the tar.gz files you started from? It looks like each of those nr.XX files you have are actually directories. Do they contain anything like the above?

You need to show us all the commands you used, including the extraction step else we're just guessing. All of the files should be present in the same directory. It looks like you may have extracted them all to separate subdirectories.

[GenoMax]

Post the full command you are using. In particular make sure you have a file called nr.pal present in the directory where you downloaded these files.

[AyehSadr]

I have this file in the directory that the files downloaded

[williamsbrian5064]

I have the same issue. Did you figure out what the problem was?

[GenoMax]

Post the complete command you are using.

[williamsbrian5064]

So I am not using a command. Similar problem to the original post, I downloaded my database (ftp://ftp.jcvi.org/pub/data/provean/nr_Aug_2011/). I extracted the files simply using tar -xzf. I am using a software the uses blast, when I run the software I get the error BLAST Database error: No alias or index file found for protein database [/path/provean/nr] in search path [/home/user::] I think maybe the issue is either, I am extracting the files incorrectly (jrj.healey) or there is some kind of issue with the database?

[GenoMax]

If you are using a database from 2011 with latest blast+ that may be a problem. If you must use that old database then you may need to find/install an old version of blast.

[Joe]

It sounds like the software you’re using requires the blast database to be in a specific location. Where are you storing the extracted files?

[williamsbrian5064]

I just made a post about this here. I figured it was the easiest way to get all the details out