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The performance of flow lines is significantly affected by the failures and the repair activities that the machines go through. The manufacturing process models based on Petri nets with time are developed for single work station, including a stochastic failure process and a repair process. The models consider two failure detection modes and three interrupted-job-handling policies. To study the influence of failures upon flow lines, the generalized stochastic Petri net (GSPN) models with two work stations are constructed for performance evaluation and simulation. A performance comparison among three cases is made. It is concluded that the repairing sequence rule considering system states exhibits much better performance in reducing the productive loss of time and cost due to failures. Finally, conclusions are drawn and some future researches are discussed.