You need to indent "fortigate_snmp" under "modules", and "walk" and the 
other keys under "fortigate_snmp".  Like the following (aside: I don't have 
any problem with formatting in the Google Groups web interface, but I'm 
using the "classic" view)

modules:
  fortigate_snmp:
    walk:
      - ifXTable
      - fgVpn        
      - fgSystem        
      - fgIntf
      - fgInetProto
    version: 3
    max_repetitions: 25
    timeout: 10s
    auth:
      username: snmpuser
      security_level: noauthNoPriv
      password: your_password                                              
                                                                            
                    




> There is no fortigate_snmp in any fortigate MIBs that I can find?
>
>
That's correct.  This is a label which prometheus' snmp_exporter gives to 
the MIB (or collection of MIBs).  You can choose whatever label you like, 
but you need to give the same label when scraping, e.g. 
target=X.X.X.X&mib=fortigate_snmp

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