You need to consider a fatigue analysis using Miner's rule. Although you quote a large number of cycles, mostwill be associated with very small waves, probably causing stresses within the endurance limit. Dependent upon the sea area, typically waves in the 4 to 12m range induce enough stress with sufficient a numbers of cycles to cause fatigue issues. Look at your wave exceedance data and consider the stresses induced by displacements related to wave height.
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I would not expect to consider a harmonic analysis for a wellhead. If there are harmonic problems predicted due to wave and current action, i.e. vortex shedding excitation on the exposed conductor tube, the design is flawed and needs more conductor guides.