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I have setup vlan trunking between fortigate firewall and catalyst 2950.
On the trunk, I am working with two interfaces. One is physical and the
other is vlan 550. Considering that physical interface is native default
vlan 1, can this configuration work? If not, why?

The interface definition of 2950 is as follows.

int fa 0/15
switchport mode trunk

int fa 0/2
switchport access vlan 550

int fa 0/4

Thanks in advance