But Jonah ran away from the Lord and headed for Tarshish. He went down to Joppa, where he found a ship bound for that port. After paying the fare, he went aboard and sailed for Tarshish to flee from the Lord.
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I believe that Jonah himself answers this question in Jonah 4:1-3. He fled when he was initially called by God because He knew that God was merciful, and would spare the Ninevites if they repented of their sin (as in fact happened). Jonah did not want to proclaim that God was going to destroy Nineveh, and then not have his prophecy fulfilled because of God showing mercy on the city as a result of its repentance. He was more concerned that he might be made to look personally foolish because of the destruction that he proclaimed not coming to pass than he was with the welfare of the Ninevites themselves. God then gave Jonah a lesson in God's own perspective through Jonah's experience with the gourd (Jonah 4:5-11).
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