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The more empathetic you are, the harder it is to do a procedure. Most any procedure involves harming a person in some way, whether by making an incision, or probing with a needle, or inserting a speculum, etc...this isn't necessarily a glaring weakness. You are just more suited for some specialties over others.
I disagree. Medical folks don't do procedures for fun, they do them because they are medically-indicated and will rule in/out important diagnostic considerations, relieve pain/discomfort, and/or prolong life. But because they can be painful or even life-threatening, perhaps the most empathetic physician will learn to do them well. I say suck it up and learn the procedures as best you can. Even if you never do it again, you never know when it will be just you in the ICU or even in the psych ward when someone needs your skills.