Place a medium pot over medium heat, then add the shallot and sauté for 2 minutes.
Add the rice to the pot and the amount of water listed on the package, then bring to a boil.
Once boiling, lower the heat to medium-low, stir and cover. Continue simmering until the rice is cooked through, as according to the directions on the package.
Peel and dice the butternut squash then spread on a baking sheet. Bake for 15 minutes then toss and bake for an additional 10 minutes. Add the pecans to the baking sheet during the last 2 to 3 minutes so they can toast.
When both rice and squash are cooked, combine in a bowl then toss with cranberries, orange zest, parsley, thyme, cranberries and black pepper. Dish can be served warm or at room temperature.