I originally ran EEMS(estimated effective migration surfaces) with a smaller dataset, and it worked fine. I then moved onto a larger dataset. I generated the new "diffs" file with the new bim/bed/fam on bed2diffs, and EEMS will not accept it. It seems to be in order - diagonal zeros, it's a perfect square, etc. The bim and fam files are in the same format as the original dataset files and produce a "diff" file. How do I pinpoint my problem? Thank you!