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It is difficult for Pi to kill his first fish because he likens himself to a murderer. Pi's character is compassionate and non-violent.
Life of Pi
Pi also found it difficult to kill the fish because he was a vegetarian.
At first pi found it difficult to kill the fish with his bare hands as the concept of killing was against his religious morals this idea is reinforced by him crying and thanking the god for coming in the form of a fish and feeding them. This shows that pi is a religious individual.