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.
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written
by
czb321 •
1 answer
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
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I think the name of the DB is
human_genome, nothuman_genome_DB, no?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 DBnameCould you try
ls human_genome*while you're in/my/path/human_genome_DBand tell us what you have in that directory?I assume
/my/path/human_genome_DBis a directory so it won't work for-db.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/:into a
blast/dbfolder and extracted the tar.gz files. From this folder I am runningthis throws the error:
So the search path seems to be correct and the downloaded db should not require a
makeblastdb. According tohuman_genome-nucl-metadata.jsonthe db name is:"dbname": "human_genome". What am I doing wrong here?I don't think
blastwill accept input from STDIN. Can you put the sequence in a file and provide via-query fileoption in your command line? With that small a sequence you may need to reduce the word size below 20.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_levelI see.
human_genomeshould work as the name since the files have that basename?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.