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!
1 answer
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.
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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.