How to define an outgroup to build a robust amino acid tree
I think you have a bug

raxmlHPC -m PROTGAMMAILG -n output.tre -o outgroup -p 10000 -s /Users)/username/Desktop/alignment_file.phy


Try the above, where username is your username. I'll check my codes later. The most important bit is the space between the -p and word outgroup. You can omit the -p 10000 it is only needed  for very geeky maximum likelihood and sets the random number stream.