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I am trying to run the standalone ncbi-blast-2.2.28+ on my machine (Mac) but get this error message when running blastp with SwissProt database:

BLAST Database error: Could not find volume or alias file (nr.00) referenced in alias file (/Users/me/bin/db/swissprot.00).

Here what I did:

1) downloaded the "ncbi-blast-2.2.28+-universal-macosx.tar.gz" from ncbi server and decompressed it

2) move the bin content of the folder to my $PATH directory "/Users/me/bin"

3) In "/Users/me/bin" I created a "db" folder, plus the ".ncbirc" file containing the following path:

[BLAST]
BLASTDB=/Users/me/bin/db

4) I downloaded the SwissProt database and got the following files in "/Users/me/bin/db/:

swissprot.00.msk
swissprot.01.msk
swissprot.02.msk
swissprot.03.msk
swissprot.04.msk
swissprot.05.msk
swissprot.06.msk
swissprot.07.msk
swissprot.08.msk
swissprot.09.msk
swissprot.10.msk
swissprot.00.pal
swissprot.01.pal
swissprot.02.pal
swissprot.03.pal
swissprot.04.pal
swissprot.05.pal
swissprot.06.pal
swissprot.07.pal
swissprot.08.pal
swissprot.09.pal
swissprot.10.pal
swissprot.pal

Then when I run blastp from any working directory (where my query file is), using this command:

blastp -query input.fasta -db swissprot

I get the following error message:

BLAST Database error: Could not find volume or alias file (nr.00) referenced in alias file (/Users/me/bin/db/swissprot.00).

As I read on other threads, I also tried to mention in the command line the whole path where the db is located, and to remove the .pal extension from the file names. But still doesn't work.

Can someone sees what I did wrong ?!!!!

lqdo2000
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4 Answers4

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you are storing your database files in db folder so you have to give this command instead of the one you have used:

blastp -query input.fasta -db db/swissprot

and I believe you are looking for an output in the console itself as you haven't used the -out option.

Also this will work only if the bin directory in which db folder is present be declared as an environment variable.

SRKR
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Have you checked the paths in .pal file?

cantalapiedra
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Swissprot database that you have downloaded contains only links to entries in nr database: "nr - Non-redundant GenBank CDS translations + PDB + SwissProt + PIR + PRF, excluding those in env_nr". So you should additionally download nr database to run the standalone blast on your machine with SwissProt database. It weighs about 20 (!) Gb, but without it your blast will not work. Here's a link: ftp://ftp.ncbi.nlm.nih.gov/blast/db/

khorms
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place all files from 00 to 10 folders into db and then check .pal file should contain 00 to 10 parts for example for nr databas its like

"nr.00" "nr.01" "nr.02" "nr.03" "nr.04" "nr.05" "nr.06" "nr.07" "nr.08" "nr.09" "nr.10"

Amarinder Singh Thind
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