How many nr database subdirectories are there?
1
0
Entering edit mode
12 weeks ago
Jessica • 0

Hi,

I am trying to download the blast nr database into my HPCC account to be blast some files. When I downloaded the nr database and tried to manually build the database, it took so long that the HPCC killed the job. Next I tried to download the subdirectories of the nr database.

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

I have been downloading these files all day. I am currently at nr.59.tar.gz and it is still downloading. Does anyone know how many subdirectories will be downloaded?

Thanks in advance!

Blast ncbi subdirectories nr • 235 views
ADD COMMENT
0
Entering edit mode

There are 59 files for download in total :) If your query sequence set is small, you can run blast without downloading the nr database: blastp -query query.fasta -db nr -remote.

ADD REPLY
0
Entering edit mode
12 weeks ago
GenoMax 120k

There are 59 (+1 nr.pal) files for nr database (not sub-directories) as of today. This set of database files are already formatted. All you need to do is keep all nr* files in one directory after you uncompress them. Set $BLASTDB variable to point to that directory and then use for blast.

ADD COMMENT

Login before adding your answer.

Traffic: 808 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6