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The RF system of CYCIAE-100 cyclotron has two cavities, which are driven separately by two identical 100-kW RF amplifiers. Due to the power on sequence issue of the three DDSs in the LLRF systems, each time when the system is individually switched on, the phase relationship may not satisfy the requirements of beam acceleration. Instead of adding an extra reset logic to the system, a search and validation algorithm based on the decision tree has been carried out to make sure the phase of the two cavities is correct right after applying power to the cavities, taking advantage of existing hardware resources. In the first year of operation, there are more than 20 times of scheduled shutdown of the cyclotron system. For each time when the cyclotron RF system is completely shutdown and powered on again, the operator confirmed that the phase matching of the two cavities can be done automatically within 30 s. The related work, including the optimization of the phase detector and the development and validation of the algorithm, is reported in this paper.