It looks like the 'system' call you are making is using a tainted variable. So it is either going to be $project->name or $force. Have you untainted them?

I am guessing that it is probably the $force variable, which looks from the name like it probably came from a command line switch. Even though you aren't using the value of $force in the system call, any expression that uses a tainted value will itself be tainted. From the perlsec docs:

The value of an expression containing tainted data will itself be tainted, even if it is logically impossible for the tainted data to affect the value.

Also, I would rewrite the system call to something like this:

my @params = ('-p', $project->name);
push @params, '-p' if $force;
system 'inc_seqs', @params;
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If you pass a string to system, it will use a shell to parse the parameter list and execute the program. If you pass a list (or array) of switches and parameters, you skip the need for the shell, and the program is executed directly, which saves the chance of any nasty shell escapes from happening.

Read the perlsec manual and it will explain how to do the actual untainting of the variables.