Keyboard shortcut (almost) never works for Automator service
In summary you will need to use:


Automator to create a service that runs your bash script
System Preferences to assign a keyboard shortcut to the service


Below are the steps involved for each. 

1. Create a service using Automator


Launch Automator (usually found within your Applications folder)
Go to File > New
Select Service and click Choose
In the top right hand of the window that appears, ensure that "No input" is selected from the Service receives drop-down list
Ensure the In drop-down list is showing "Finder"
In the second column containing the long list, find "Run Shell Script" and double-click on it
This will add the Run Shell Script window on the right
Within the Run Shell Script section ensure you have selected the "/bin/bash" option for your Shell
Now add your code 
Save the service using a meaningful name (e.g. Take Reference Screenshot).


Now to the next step.

2. Creating your shortcut


Go to System Preferences > Keyboard > Shortcuts
Select Services from the sidebar
Find your service (it'll be in the list on the right-hand side)
Add a shortcut by double clicking on the service name
Now go to System Preferences > Security &amp; Privacy > Privacy
Select Accessibility in the sidebar
Click on the + sign (you may need to unlock the padlock if it's locked)
Add Automator.
Add Finder (to find this you will need to navigate to /System/Library/CoreServices/Finder.app).
Exit your System Preferences.


Let me know how you go.