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This looks like a duplicate of How to visualize a real robot in Rviz, but just to reiterate:

If you have a node that already publishes joint states for your real robot, then you don't need to start joint_state_publisher.

An instance of joint_state_publisher is only needed if:

1. you don't have another node that publishes JointState messages and you want to fake them (use_gui:=true)
2. you have multiple publishers of JointState messages and want to aggregate them (source_list:=[..])

[..] I don't know how to resolve the conflict between my own node and joint_state_publisher node [..]

Just don't start joint_state_publisher (but see the points above).