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This article explains that Copper transceiver will cause status problem and how to fix this issue.

When using old copper transceiver with SKU: FG-TRAN-GC with FortiGate, sometimes user will experience wrong status when the speed and duplex is set manually.

For example:
When the speed and duplex is set manually if the connected switch have port down, on FortiGate the interface status is up.

In the above case port7 is has manually set as 1000F and connected switch has port down however, the FortiGate sill detects it as up.

For the reason is that this copper transceiver does not support link indication feature.

A new copper transceiver with SKU FN-TRAN-GC has been released for this.

As a workaround, it is possible to set the speed as auto-negotiation.