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In this paper, we focus on automated manufacturing systems composed of AGVs as material handling devices and jobshop layout of machines. AGV carries the raw materials through the shops in batches. In each shop an inspection unit is configured (multi stage inspection). Considering the size of the batches and the defect rate, one type of the inspection (sampling inspection or full inspection) is carried out. Number of defects in products is a random variable which specifies the inspection policy. In general inspection incurs cost to our system. Machines in each shop are in parallel case. The reliability of machines follows a probability distribution. Shops are in series case. Hence, a composite (parallel-series) system is ensued. While the reliability of machines decreases, numbers of defects in products increases and as a result incur more costs to the system. The aim is to control the number of defects in a way that satisfies both product assurance level which is a consequence of inspection and machines reliability lower limit considering the available operational budgets.