Yes I was able to figure out what the issue was. To be sure, and to possibly help others in the future with creating an edge matrix, here are the steps I believe are necessary to make a binary edge file:

1. Make a matrix that is NxN dimensions, where N is the number of nodes you specified in your node file.
2. The matrix is populated with 0s and 1s, where 1 indicates an edge and 0 indicates no edge.
3. Each row and column corresponds to the order that you wrote your nodes out in the node txt file. E.g., if you want an edge between node 1 and 3, you would place a 1 in the matrix at cell {1, 3}.

Does this seem correct? Thank you for your assistance.

Best,
Dina