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Old 05-24-2015, 07:57 AM   #1
gt259
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Default BLAST Database error: No alias or index file found for protein database

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;

[email protected][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
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Old 05-24-2015, 01:28 PM   #2
GenoMax
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Location: East Coast USA

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Posts: 6,780
Default

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?

Code:
$ ls -lh /media/sf_F_DRIVE/nr*
Are these files readable by all? Otherwise try

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

Last edited by GenoMax; 05-24-2015 at 01:30 PM.
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Old 05-24-2015, 11:31 PM   #3
rhinoceros
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By nr directory do you mean that you have the unzipped files in:

Code:
/media/sf_F_DRIVE/nr/*
instead of

Code:
/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"
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