I was getting the same issue :
[INST STDERR] Instruments Trace Error : Target failed to run: Permission to debug was denied. The app must be signed with a development identity (e.g. iOS Developer).
Solution:
1. I archived the the app with Debug Developer Profile in xcode for device.
2. The go to Window -> Organiser -> to see all the list of archieves
3. Now select the archive to wanted to export and open it in finder
4. Right click and show package contents
5. Go to the Products/Applications folder
You will see the .app file.
Use this instead of the ipa.
Make sure that the device has been already added to the developer portal and all the certs are installed on it for the above steps to work.
Once this is in place. Also, make sure you get the ios-webkit-debug-proxy from the link below:
https://github.com/appium/appium/blob/master/docs/en/advanced-concepts/ios-webkit-debug-proxy.md
Also, enable developer tools on on the device setting.
Also, make sure safari webinspector (safari -> Develop) -> Inspector is on
Hope it helps:-)
NOTE: When you want appium to install the app on the device for you, don't provide Bundle ID.