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Following a successful period of data-taking between 2006 and 2011, the Virgo gravitational-wave detector was taken offline for a major upgrade. The changes made to the instrument significantly increased the complexity of the control systems and meant that an extended period of commissioning was required to reach a sensitivity appropriate for science data-taking. This commissioning period was completed in July of 2017 and the second-generation Advanced Virgo detector went on to join the Advanced LIGO detectors in the O2 science run in August of the same year. The upgraded detector was approximately twice as sensitive to binary neutron star mergers as the first-generation instrument. During the August 2017 science run, Advanced Virgo detected its first gravitational wave signal, with the binary black hole merger, GW170729. This paper describes the control of the longitudinal degrees of freedom in the Advanced Virgo instrument during the O2 science run and the process that brought the detector from an uncontrolled, non-resonant state to its target working point.