Well you are doing var cube1 = new Cube1(); which is how you would make an object in C#, but since it is Unity, and this is a MonoBehaviour, you are not supposed to make it like that.

Instead, make a new GameObject and attach the Cube1 script to it.

void Start()
{
    // make a new gameobject.
    GameObject gameObject = new GameObject();

    // attach a Cube1 script to it. note: by doing Cube1 cube = ... as Cube1;
    // cube now holds a reference to the script you added.
    Cube1 cube = gameObject.AddComponent<Cube1>() as Cube1;

    // call the function on that cube.
    cube.Rectangle();
}

Sidenote, if you don't make an object in the scene that holds the ClockController, it won't execute the Start() method.

When you already have an existing GameObject (instead of making a new one) that has a script you want to access, you can use gameObject.GetComponent<Cube1>() , store it in a variable (if necessary) and access it that way. You just need to get that specific GameObject to begin with.

Well you are doing var cube1 = new Cube1(); which is how you would make an object in C#, but since it is Unity, and this is a MonoBehaviour, you are not supposed to make it like that.

Instead, make a new GameObject and attach the Cube1 script to it.

void Start()
{
    // make a new gameobject.
    GameObject gameObject = new GameObject();

    // adding a SpriteRenderer as your `Cube1` will try to access it. 
    // -- please also see the bottom note of the answer. --
    gameObject.AddComponent<SpriteRenderer>();

    // attach a Cube1 script to it and store the reference to it in a var. 
    Cube1 cube = gameObject.AddComponent<Cube1>();

    // call the function on that cube.
    cube.Rectangle();
}

Sidenote, if you don't make an object in the scene that holds the ClockController, it won't execute the Start() method.

When you already have an existing GameObject (instead of making a new one) that has a script you want to access, you can use gameObject.GetComponent<Cube1>() , store it in a variable (if necessary) and access it that way. You just need to get that specific GameObject to begin with.

Extra info on component dependencies:

As pointed out by @DMGregory, cube.Rectangle() will try to find/access a SpriteRenderer on the cube object, which would have to be added first. You could add [RequireComponent(typeof(SpriteRenderer))] which means that whenever you add a Cube1 script to a GameObject, the required component is added aswell if it is not already there.

I'd suggest to take a look at the docs: https://docs.unity3d.com/ScriptReference/RequireComponent.html

Alternatives would probably be making sure in your Cube1 script that at some point a SpriteRenderer is attached, but that's all going off-topic I think.