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got up to run away from the presence of Yahweh
"ran away from Yahweh." "got up" is referring to Jonah leaving where he was. (See: rc://en/ta/man/translate/figs-idiom)
the presence of Yahweh
Here Yahweh is represented by his presence. (See: rc://en/ta/man/translate/figs-metonymy)
go to Tarshish
"and went to Tarshish." Tarshish was in the opposite direction to Nineveh. This can be made explicit. AT: "went in the opposite direction, toward Tarshish" (See: rc://en/ta/man/translate/figs-explicit)
He went down to Joppa
"Jonah went to Joppa"
ship
A "ship" is a very large type of boat that can travel on the sea and carry many passengers or heavy cargo.
So he paid the fare
"There Jonah paid for the trip"
boarded the ship
"got on the ship"
with them
The word "them" refers to the others who were going on the ship.
away from the presence of Yahweh
Here Yahweh is represented by his presence. AT: "away from Yahweh" (See: rc://en/ta/man/translate/figs-metonymy)