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Destroying assets is not permitted to avoid data loss. If you really want to remove an asset use DestroyImmediate (theObject, true); UnityEngine.Object:Destroy (UnityEngine.Object) XNode.NodeGraph:Clear () (at Assets/Scripts/xNode-1.8.0/Scripts/NodeGraph.cs:51) XNode.NodeGraph:OnDestroy () (at Assets/Scripts/xNode-1.8.0/Scripts/NodeGraph.cs:83) This can be caused by destroying instantiated NodeGraph. Fixed by instantiating nodes in Awake.