Hi all,

I'm trying to do a blast to local NCBI nt database in Linux. The code I've used to download and decompress the DB is:

cd /volume/BlastDBs

update_blastdb.pl nt
update_blastdb.pl taxdb

gunzip *tar.g*

ls *.tar |xargs -n1 tar -xvf

Notes: I needed to do a loop as tar will only do one file at a time I noticed that the .md5 suffix files not recognised -> was ignored by gunzip This folder has files with the following extensions for each 'piece' of the DB:

.tar
.tar.gz.md5
.nhd
.nhi
.nhr
.nin
.nnd
.nni
.nog
.nsd
.nsi
.nsq

There is also an nt.nal file

The taxdb has:

.tar
.tar.gz.md5
.btd
.bti

Doing the blast (I tried with the full path to the DB, and using the -nt parameter, got the same error message both times):

blastn -db /volume/BlastDBs -query /volume/Assembly_data/Test/Test.fasta -outfmt 6 -out TEST_blastn.tabular

I get the error message:

BLAST Database error: No alias or index file found for nucleotide database [/volume/BlastDBs] in search path [/volume/Assembly_data/Test:$/volume/BlastDBs:]

As a way of troubleshooting, I created a small DB from a fasta file using the following script:

cd /volume/Assembly_data/Test/TestDB

makeblastdb -dbtype nucl -in /volume/Assembly_data/Test/Test.fasta -title Test_db -out Test_db

It seemed to work and created 3 output files in the TestDB directory: Test_db.nhr Test_db.nin Test_db.nsq

Then ran the blast using:

blastn -db /volume/Assembly_data/Test/TestDB -query /volume/Assembly_data/Test/Test.fasta -outfmt 6 -out TEST_blastn.tabular

Got the same error message. ..............................

I don't know if it's important, but I installed blast using:

conda install blast

Any suggestions about what could be going wrong are greatly appreciated. It's doing my head in.

Cheers, Kelli