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

Question

[czb321]

Hi,

I have an issue it has been already discuss here a lot, but I cannot find what i'm doing wrong..

For a blastn alignement against the human_genome DB I downloaded the database from the NCBI:

wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/human_genome.*.tar.gz

decompress the files:

for a in human_genome.*.tar.gz; do tar xzf $a; done

Obtaining the index file : GCF_000001405.38_top_level.nal

I setup the BLASTDB

 BLASTDB=/my/path/human_genome_DB/

 blastn -query /my/path/final_assembly.fasta -db human_genome -out /my/path/host.txt

And get this error:

 BLAST Database error: No alias or index file found for nucleotide database [human_genome] in search path.

I also tried with -db /my/path/human_genome_DB but didn't work.- db GCF_000001405.38

I perform the same procedure with the nt database and it works .. do you have any idea what I'm doing wrong?

Thanks.

[5heikki]

I think the name of the DB is human_genome, not human_genome_DB, no?

[lieven.sterck]

did you check the blastDB name is correct? (seems to but best to check anyway)

In your blastDB dir look for a file with extension .pal , that basename is your DBname

[gernophil]

I know this is quite some old thread, but I am having the exact same problem right now and I can't seem to find the answer here.

I downloaded these files from https://ftp.ncbi.nlm.nih.gov/blast/db/:

human_genome-nucl-metadata.json
human_genome.00.tar.gz
human_genome.00.tar.gz.md5 
human_genome.01.tar.gz
human_genome.01.tar.gz.md5

into a blast/db folder and extracted the tar.gz files. From this folder I am running

echo ">seq1\nAAAAAACAGCTTCAACTCCG" | blastn -db human_genome -dust no -word_size 20

this throws the error:

BLAST Database error: No alias or index file found for nucleotide database [human_genome] in search path [/[path_deleted]/blast/db::]

So the search path seems to be correct and the downloaded db should not require a makeblastdb. According to human_genome-nucl-metadata.json the db name is: "dbname": "human_genome". What am I doing wrong here?

[GenoMax]

I don't think blast will accept input from STDIN. Can you put the sequence in a file and provide via -query file option in your command line? With that small a sequence you may need to reduce the word size below 20.

[gernophil]

It does indeed. It works with -remote. I found the error though. I put the db files from .00 and .01 in different folders, but they should be in the same. And the name of the database is: GCF_000001405.39_top_level

[GenoMax]

I see. human_genome should work as the name since the files have that basename?

[gernophil]

Haven't used CLI blast in a while. I just thought human_genome was right since it was in the .json file :). Guess it just shouldn't work.

Answer 1

[czb321]

Thanks a lot for your reply.

I checked for the name of the database again and the version of blastn I've installed. The last version of blastn I think needs a newer database format, in my case the human_genomic_v4 database. I downloaded and tried this one and it works.

Maybe this link can also help anyone :) ftp://ftp.ncbi.nlm.nih.gov/blast/db/v4

Regards

[GenoMax]

Default blast database format is now v5 and is needed by current blast+. What you downloaded was the OLD database format. Please be aware that v4 databases that you downloaded are not updated (last update was in February 2020).