BLAST Database error: No alias or index file found for protein database

[gt259]

Hi Chris,

I am having a similar problem to your original post but unfortunately your workaround hasn't worked for me, do you have any other suggestions?

Im running off Biolinnux8 (Ubuntu14.04), I downloaded the whole pre-formated nr database via ftp from ftp://ftp.ncbi.nlm.nih.gov/blast/db/

I ran this command;

graham@graham-VirtualBox[graham] blastp -query Dropbox/PhD/Bioinformatics/Organism_sequences/Nosema_ceranae/test.fasta -db /media/sf_F_DRIVE/nr -out blastp_out_1e-05.txt -evalue 1e-05

and got this error;

BLAST Database error: No alias or index file found for protein database [/media/sf_F_DRIVE/nr] in search path [/home/graham:/var/lib/blastdb]

Following your recommendation I updated the PATH and ran;

setenv BLASTDB /home/graham:/var/lib/blastdb:/media/sf_F_DRIVE/nr

but it didn't seem to work and I get this message;

BLAST Database error: No alias or index file found for protein database [/media/sf_F_DRIVE/nr] in search path [/home/graham:/home/graham:/var/lib/blastdb:/media/sf_F_DRIVE/nr:]

the nr directory has all sub databases 00-32 including file extensions phd,phi,phr,pin,pnd,pni,pog,ppd,ppi,psd,psi,psq & tar.gz.md5.

Any and all help appreciated.
Graham

[GenoMax]

Looks like you have done all the right things but it appears that blast is not able to read from that directory (which appears to be on an external drive).

Are you able to get a listing by?

$ ls -lh /media/sf_F_DRIVE/nr*

Are these files readable by all? Otherwise try

$ chmod a+r /media/sf_F_DRIVE/nr*

[rhinoceros]

By nr directory do you mean that you have the unzipped files in:

/media/sf_F_DRIVE/nr/*

instead of

/media/sf_F_DRIVE/*

If yes, there's your problem. You should provide the full path, e.g. in the case of the former "/media/sf_F_DRIVE/nr/nr"