MIAMI — By the time the cargo ship El Faro pulled out of the busy port in Jacksonville, Fla., last Tuesday ready to begin its routine 1,200-mile run of goods to San Juan, P.R., Tropical Storm Joaquin, as it had been recently christened, was threatening to become a hurricane.

For many experienced captains of large vessels, a tropical storm, even one that is strengthening, is cause for concern but not necessarily alarm. Such storms in the Caribbean, along Hurricane Alley, are commonplace and carefully monitored, and do not necessarily lead to canceled voyages, veteran captains said.

But by the time El Faro and its 33 crew members approached the Bahamas, the storm had turned treacherous more quickly than anticipated. It hurdled past hurricane Categories 1, 2 and 3 until it settled at 4, a fearsome ball of wind, waves and rain, and then it sat. By Thursday, El Faro was trapped in the crush of 50-foot seas and winds of 125 miles per hour, near the eye of the hurricane. Listing dangerously 15 degrees, the ship, full of cargo containers and cars, was taking on water. The engine failed, making it impossible to steer. Then, after a distress signal, all communication vanished at 7:20 a.m.

On Monday morning, the Coast Guard here said it feared the worst: “We believe it sank in the last known position that we recorded on Thursday,” about 35 miles northeast of Crooked Islands, the Bahamas, in 15,000 feet of water, Capt. Mark Fedor said. “We are still looking for survivors or any signs of life or any signs of that vessel.”