The thermodynamics of the $SU(4)$ gauge theory with a single flavor of fundamental quarks is analyzed on the lattice with dynamical fermion simulations, which is the low-energy sector of a realistic, strongly-interacting dark matter model—the Hyper Stealth Dark Matter. The gravitational wave spectrum from the first-order confinement transition in the early universe is further calculated, where the effect of the dark sea quarks, which decrease the interface tension in the effective potential of the Polyakov loop, is shown numerically to lower the gravitational wave amplitude.