I’m not sure if AS400 FTP has additional commands which a normal FTP server has, but assuming that it doesn’t, you pretty much can’t. FTP designed to transfer files from server to server (or workstation to server), not for launching applications on the server’s OS. I know that one method which is often used is to after the large data has been uploaded, upload another file as a trigger file. The trigger file is usually a very small file. You can then setup a job on the server which looks for this file. If the file doesn’t exist then the job does not continue. Once the file exists the rest of the job or application kicks off and processes the file. After the main processing is completed the trigger file is deleted so that the application doesn’t run again until the next file is uploaded.
The i5/OS FTP client supports the QUOTE subcommand which allows you to send commands for execution on the FTP server. These subcommand include RCMD for remote command execution. This command could then call/submit a program.