A method includes pumping fluid from outside of a downhole tool through a flowline of the downhole tool with a pump and taking first measurements, using at least one sensor, within the flowline during a first stage of pumping the fluid. The method further includes estimating a saturation pressure of the fluid, via a processor, based on the first measurements and a saturation pressure model generated based on second measurements taken using the at least one sensor during a second stage of pumping the fluid, and operating the pump to maintain a fluid pressure in the flowline greater than the estimated saturation pressure.
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