For the first parameter the program is expecting a Uniform Sequence Address or USA to tell it where to find a sequence on which to work. A list of parameter types can be found here . The values must be in the right order though otherwise you will probably get an error, or worse have the wrong output. Mandatory qualifiers are the inputs the program needs in order to run. Optional qualifiers allow you finer control over how the program runs but will only be used by more advanced users.
Advanced qualifiers are for the real expert user.
These are not normally needed for normal use but are there for the specialist user when they need them. General qualifiers are those which apply to all programs. A table can be found here Associated qualifiers are qualifiers associated with parameter typoes that allow you fine control over a parameter. Option Type Description -auto bool Do not promt for input. The program will run without asking for any input, taking the values given on the command line or the default values if no value was given on the command line.