Here are a few tips to download the data with wget. 

# NOTE: always have a trailing / after the target directory that you want to download. 
# e.g. specify 
# https://genome.senckenberg.de/download/TOGA2/Genomes/Mammalia/
# and not 
# https://genome.senckenberg.de/download/TOGA2/Genomes/Mammalia


# to download the entire Genomes or GenomeAlignments or TOGA2 directory, use these commands with --cut-dirs=2
wget -e robots=off --recursive --no-check-certificate --no-parent --no-host-directories --reject "index.html*" --reject "robots.txt" --directory-prefix=./ --cut-dirs=2 https://genome.senckenberg.de/download/TOGA2/Genomes/

wget -e robots=off --recursive --no-check-certificate --no-parent --no-host-directories --reject "index.html*" --reject "robots.txt" --directory-prefix=./ --cut-dirs=2 https://genome.senckenberg.de/download/TOGA2/GenomeAlignments/

wget -e robots=off --recursive --no-check-certificate --no-parent --no-host-directories --reject "index.html*" --reject "robots.txt" --directory-prefix=./ --cut-dirs=2 https://genome.senckenberg.de/download/TOGA2/TOGA2/



# to download a subdirectory, here Genomes/Mammalia, set --cut-dirs=3
wget -e robots=off --recursive --no-check-certificate --no-parent --no-host-directories --reject "index.html*" --reject "robots.txt" --directory-prefix=./ --cut-dirs=3 https://genome.senckenberg.de/download/TOGA2/Genomes/Mammalia/


# to download only a specific species (here Rice whale), set --cut-dirs=4
wget -e robots=off --recursive --no-check-certificate --no-parent --no-host-directories --reject "index.html*" --reject "robots.txt" --directory-prefix=./ --cut-dirs=4 https://genome.senckenberg.de/download/TOGA2/Genomes/Mammalia/Balaenoptera_ricei__Rices_whale__HLbalRic2__GCF_028023285.1/