I want to download all available genomes of multiple bacterial and archeal genera.
Downloading the genbanks for a single species is relatively easy (if you already know the exact folder_name on the ftp-server.
to get all genbank-files associated with methanococcus maripaludis C5.
However, what is driving me crazy is trying to go though the genomes-subfolders recursively using wildcards. For example if I want to get ALL genbanks of ALL methanococcus species (or if i did not want to find out the exact folder names by hand) something like:
"wget -A .gbk ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Methanococcus*"
This always gives me error messages. but I KNOW its possible in principle. I found these Instructions on Github for exactly the task i want, but they do not seem to work (perhaps the wget syntax has changed?)
wget -cNrv -t 45 -A *.gbk,*.fna "ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Genus_species*" -P ."
Can anybody please tell me what I'm doing wrong?