Entering edit mode
4.0 years ago
geosmin
▴
20
I installed the blast+ program on my computer to use BLAST locally. I also downloaded the complete nr database to my external hard drive (D:\blastdb). To access it I created an environment variable called BLASTDB with the path to my external hard drive, as was explained in the official user manual.
When I try to update the nr database with the command prompt:
update_blastdb.pl --decompress nr
it downloads it to the current working directory. When I try to do it in D:\blastdb, I get an error. When I just try to run a blast search like this:
blastp -out test.xml -outfmt 5 -query query.fasta -db nr
in D:\blastdb, it takes forever.
yes, that behaviour of update_blastdb.pl is correct as it purpose is to download and unpack the blastDBs offered by ncbi.
if you already have downloaded the DBs there is no need to run update_blastdb.pl again. SImply untar&unzip the downloaded version and it should work (you will need some storage to put them though)
It seems that the blast itself is working OK though, but indeed if you use the DB put on the external drive it might (/will) take forever as most likely that external disk is not fit to run such kind of operations. To have some serious speed increase you should store the DBs on a more performant disk.
Thank you very much for your answer! I was just confused why blast+ is not able to access my external hard drive on its own, after setting the BLASTDB environment variable. Apparantly you need to use the
makeblastdbcommand on the unzipped files to create the database? At least that's what I was told by a Phd student. Have you ever used such a local database? I was unsure what kind of hardware to use. A friend suggested a network assisted storage system.depends, if you downloaded the preformatted version of the DBs you only need to untar/zip them. If you downloaded the fasta file then indeed you first need to run makeblastdb on it.
Yes, I often (nearly only) use local DBs, however I work exclusively in linux environment. Indeed NAS storage will perform much better indeed, also the build-in HDs of your desktop/laptop will already perform better than an external drive.
are you in a linux or windows environment?
I'm using windows 10.