How to download the whole BLAST nt database into a specific folder? I have successfully downloaded the whole nt BLAST database into the current folder using:

wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz" 


However, I would like to download it in a specific folder, e.g. output/

I have tried:

wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz"  -O output/


but it does not work. Nothing happens. My 'wget-log' is empty.

I could move to that folder and download it there but I would like to remain in the same working directory.

C.
-O is to specify the name of the output file. You want the -P option.

So, from your example

wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz" -P output/