This is not an error but a warning. Apparently your trimmer cuts of most of the read because of an adapter detection or low-quality of the base pairs. It would be smart to discard reads shorter than a certain cutoff, e.g. 20bp categorically as they have little change to be properly aligned (which most trimmers do by default), simply because of the size. The shorter the size, the more likely they will be multimappers. A 2bp read cannot be aligned anyway, as one might imagine quiet well. Please post the full command of the trimming.