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According to Roskosmos, the accident led to the unplanned separation between the third stage of the launch vehicle and the spacecraft. Members of the commission established that the most probable cause of the accident had been the disintegration of the oxidizer tank of the third stage as a result of the failure of the 11D55 engine, following the fire and disintegration of its oxidizer pump, Roskosmos said. The fire in the pump and its disintegration could be triggered by a possible injection of the foreign particles into the pump’s cavity or by violations during the assembly of the 11D55 engine, such as a wrong clearance between the pump’s shaft and its attachment sleeve, floating rings and impellers, leading to a possible loss of balance and vibration of the rotor.
The fault, which has a production nature, manifested itself during the flight, Roskosmos said. The State Corporation promised to prepare a plan of immediate action at enterprises of the the rocket industry to ensure the safe launch of the Progress MS-05 spacecraft, Roskosmos announced. [emphasis mine]
It appears that though they have not definitely established what went wrong (due to a lack of telemetry), they have determined that all of the possible causes are related to quality control issues.