Probably best to use && instead, as: system("command1 && command2 && command3") so that if command1 fails, command2 and 3 won't excecute. This is useful if further commands depend on previous commands (or could have bad consequences if they aren't executed).

A better way would be to write a shell script that takes 2 arguments and then call that from perl. Ie:

script.sh #!/bin/bash /PATH/initialize_system
/PATH/skew.k $1
/PATH/savegif.k $2

And then your perl script just runs:

system("script.sh $arg_for_frame_number $frame_number");

I guess the shell script could be perl too, but there is more than one way to do it :)