EKF failsafe was triggered while Variances did not reach FS_EKF_THRESH

We are trying to arm and takeoff the copter in guided mode by mavros and got “Err: EKF Failsafe” while the copter was armed at guided mode.
But when we check the EKF variances in dataflash log, none of SP, SV, SM have ever reach FS_EKF_THRESH.
Just like this:

Here is our dataflash log: logs/80-01-01_08-00-00_3.bin at main · JC-hub/logs (github.com)
And here is our rospy script: logs/test_realworld.py at main · JC-hub/logs (github.com)

Firmware Version: ArduCopter V4.0.7 (0bb18a15)
Copter Version: Hex 450 edu