You will always need to run Nemesis (using steps 8 to 16) after running FNIS. If you keep adding or removing human animations, you will never need to run FNIS again.
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You'll only need to run FNIS when you install / remove creature animations. If you look through the list of esp, you should find a new "FNIS.esp" (generated inside "Nemesis output"). Nemesis will create a FNIS patch for the animations it couldn't process. "FNIS" is the only mod that should be disabled. Step 16: Keep "FNIS Output", "Nemesis" and "Nemesis Output" enabled. You'll have to wait until a message pops up, showing how much time the process took. The big bar in the center isn't a progress bar but it shows how many animations you're using. Step 15: Nemesis will take a little while and will inform you once it is done. Once it is done, you can then click on "Launch Nemesis Engine". Step 14: Everytime you install or remove animations, you'll need to click on "Update Engine" first. Step 11: Enable both "Nemesis" and "Nemesis Output". Step 8: Enable both "FNIS" and "FNIS Output". In order to run both FNIS and Nemesis, you need to carefully follow these steps: If FNIS Output has a priority value of "10", Nemesis Output should then have a priority above "10"). Nemesis Output should overwrite everything from FNIS Output and FNIS creature (even though there shouldn't be anything from Nemesis overriding the creature animations), meaning you should assign a higher priority to Nemesis Output (if you don't know what this means, 0 is the lowest priority, 99999 is a very high priority. You've now properly installed both FNIS and Nemesis. Step 7: Repeat steps 4 to steps 6 with Nemesis instead of FNIS (should be in ".v0.84-betaNemesis_EngineNemesis Unlimited Behavior Engine.exe"). Step 6: Check "Create files in mod instead of overwrite", open up the dropdown list at the right of the option and find "FNIS Output". Step 5: Add an executable using "Add from file" and go find FNIS's executable (should be in "modsFores New Idles in Skyrim SE - FNIS SEtoolsGenerateFNIS_for_UsersGenerateFNISforUsers.exe") Step 4: Open up MO2, click on the dropdown list at the top right (next to "Run") and click Edit. Leave both FNIS and Nemesis disabled, for now. Step 3: Activate both "FNIS Output" and "Nemesis Output". Step 2: Create two folders, one named "FNIS Output" and the other "Nemesis Output". You'll never need to disable FNIS creature pack ever. Enable "FNIS creature pack" and leave it enabled permanently. Step 1: Install FNIS, FNIS creature pack and Nemesis.
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If you use MO2, here's a great guide from LoversLab for how to do it: I've been running FNIS and Nemesis successfully for a while now.