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Encrypting a rooted Android 6.0.1 device enables some of the features that official apps have

Most users want to root their Android OS to gain more control over the device. However, doing so may disable the encryption of the device, which may cause official apps to misbehave. An Android enthusiast posted a solution on Reddit about the fix and states that it worked on his Nexus 5 (hammerhead) MOD. However, we recommend novice developers to be cautious as it may soft brick the device. Create a backup of the data along with a factory image to restore the device to its stock OS.
We also recommend users to charge their device to at least 75% before starting the encryption process. Users should ensure that a reliable data cable is used to transfer the file to ensure that the required files are not copied with errors. This process worked with Nexus 5 Hammerhead Mod and SU Binary 2.66 version.
How To Encrypt Android 6.0.1 Rooted Device

Step#1: 
Flash the stock boot image that is extracted from the factory image file provided by Google in the developer’s site. Extract the main zip file that contains the factory image and place it in the root folder of the device.


Step#2:
  Boot the device in extraction mode by pressing and holding the volume down and power button, simultaneously. After the installation, boot the device so the extracted file enables device encryption.


Step#3:
 Reboot the device and flash the super user (SU) binary. The Android enthusiast stated that he used SU binary 2.66. This step will modify the boot image and cause the device to reboot numerous times. The user would have to input the encryption password each time.Continue the steps till the device reboots successfully into the OS. This implies that encryption has been successfully completed.

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