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I am facing a problem in Raspberry Pi Robot.

Whenever I reboot the Raspberry Pi, some of the pins are by default configured as HIGH. Because of this, Raspberry Pi Robot fails to function correctly during the startup/shutdown sequence.

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The simple answer is you can't.

All the GPIO pins start as inputs see https://raspberrypi.stackexchange.com/a/38059/8697 and also https://raspberrypi.stackexchange.com/a/59216/8697

You need to design your interfacing circuitry properly (maybe less beeer), e.g. with appropriate pullups or pulldowns. NOTE the I²C pins have low onboard pullups.

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