It clearly says permission issues
Your mongod wt files should be owned by mongod but they are all owned by your user id and the timestamps look very old
Did you have a working mongodb before at same dbpath?
Better to clean dbpath,logpath,tmp files and restart with service if you don’t need those old files
Regarding manual run just give your home dir or create a test dir under your home dir and give full permissions
Whichever dirpath you give your mongod should be able to write to it
Also check this thread.Not a Mac install but concepts are same regarding ownership/permissions etc