I think your
? gets interpreted by shell (Correction by vinc17: more likely, it's the
& which gets interpreted).
Just try with simple quotes around your URL:
Note that the file you are requesting is a
.tar file but the above command will save it as
index.html?acc=GSE48191&format=file. To have it correctly named, you can either rename it to
mv 'index.html?acc=GSE48191&format=file' GSE4819.tar
Or you can give the name as an option to
wget -O GSE48191.tar 'http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191&format=file'
The above command will save the downloaded file as