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Manuel Cascallana, who is currently the assistant coach, will be the interim coach.
The Indian Super League side drew 1-1 against 10-man Bashundhara Kings of Bangladesh to reach the next round.
The Spaniard guided the Mariners to the final in their first-ever ISL season only to lose the title to Mumbai City FC.
Kolkata heavyweights ATK and Mohun Bagan who came together to become a new identity - ATK Mohun Bagan - will be playing their first ISL season as defending champions.