reported a frozen door seal, and abnormal noises coming from the right aft service door. They requested a full inspection of the door. The inspection was carried out by a ground engineer, who then performed a pressurization leak check. In order to carry out this check without requiring the aircraft's engines, the pressurization system was set to "manual". However, the engineer failed to reset it to "auto" on completion of the test. After the aircraft was returned into service, the flight crew overlooked the pressurization system state on three occasions: during the pre-flight procedure, the after-start check, and the after take-off check. During these checks, no one on the flight deck noticed the incorrect setting. The aircraft took off at 09:07 with the pressurization system still set to "manual", and the aft outflow valve partially open. As the aircraft climbed, the pressure inside the cabin gradually decreased. As it passed through an altitude of , the cabin altitude warning horn sounded. The warning should have prompted the crew to stop climbing, but it was misidentified by the crew as a take-off configuration warning, which signals that the aircraft is not ready for take-off, and can only sound on the ground. The alert sound is identical for both warnings. In the next few minutes, several warning lights on the overhead panel in the cockpit illuminated. One or both of the equipment cooling warning lights came on to indicate low airflow through the cooling fans (a result of the decreased air density), accompanied by the master caution light. The passenger oxygen light illuminated when, at an altitude of approximately , the oxygen masks in the passenger cabin automatically deployed. Shortly after the cabin altitude warning sounded, the captain radioed the Helios operations centre and reported "the take-off configuration warning on" and "cooling equipment normal and alternate off line." He then spoke to the ground engineer, and repeatedly stated that the "cooling ventilation fan lights were off." The engineer (the one who had conducted the pressurization leak check) asked: "Can you confirm that the pressurization panel is set to AUTO?" However, the captain, already experiencing the onset of hypoxia's initial symptoms, disregarded the question, and instead asked in reply, "Where are my equipment cooling circuit breakers?" This was the last communication with the aircraft. The aircraft continued to climb until it leveled off at FL340, approximately . Between 09:30 and 09:40, Nicosia ATC