"We are called upon to show mercy and forgiveness, even in the face of great evil and suffering, but we are also called upon to repent and do penance," the bishops said.
They noted the South Sudanese Catholic participation in the April 2016 non-violence conference co-sponsored by the Pontifical Council for Justice and Peace and Pax Christi International. They repeated their statements that civil war in South Sudan has no moral justification.
The bishops voiced support for the transitional government and asked those with reservations about a conflict resolution agreement to overcome them.
"Reservations are not grounds for rejecting the agreement. Only when we have stopped killing ourselves can we sit down together to rebuild the nation," they said.
They encouraged the transitional government's efforts to secure a comprehensive ceasefire, to improve basic services and the economy, and to resolve the humanitarian crisis. The bishops also thanked the international community for assistance.
In their letter, the bishops especially remembered Sister Veronika Theresia Rackova, a Slovakian nun who died after being shot by soldiers of the Sudan People's Liberation Army.
"In the eyes of the people whom she served she is already a martyr. May she rest in peace," they said, adding that she is only one of the thousands of victims killed in "this senseless conflict."
They warned that the SPLA is different from the army that had defended the country in its efforts to secure independence from Sudan. They said the army had poor discipline, training, and leadership, and that it preys upon the population, rather than protecting them.
The bishops also expressed concern about robberies of churches and church personnel.
Pope Francis' apostolic exhortation Amoris laetitia was also a topic. The bishops cited its comments on problems that families face in countries like South Sudan: a lack of decent housing, a lack of work and possibilities for the young, the violence of war, terrorism, organized crime, youth homelessness and forced migration.
The Pope praised various African countries' traditional values and strong marriages that bind families together, the bishops noted.
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"May the strength of our South Sudanese families be a resource for peace and reconciliation in our nation," the bishops concluded.