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Output from Nexus Root Toolkit v2.1.9

Rebooting your device into bootloader mode...
adb reboot bootloader

Checking Fastboot Connectivity
fastboot devices
ENU5T15B05003467    fastboot
 + Fastboot Device Connected

 + Confirmed: Bootloader Unlocked.
Flashing Custom Recovery to RECOVERY partition...
fastboot flash recovery "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Recovery_Custom\TWRP\twrp-3.0.2-2-angler.img"

Temporarily Booting TWRP...
fastboot boot "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Recovery_Custom\TWRP\twrp-3.0.2-2-angler.img"

Checking ADB Recovery Connectivity
adb devices
ENU5T15B05003467    recovery
 + ADB Recovery Device Connected

Pushing root files to your device:
Pushing "SR1-SuperSU-v2.78-SR1-20160915123031.zip" to your device:

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\SR1-SuperSU-v2.78-SR1-20160915123031.zip" "/sdcard/!ReadyToFlash/Root_Files/SR1-SuperSU-v2.78-SR1-20160915123031.zip"

100%  /sdcard/!ReadyToFlash/Root_Files/SR1-SuperSU-v2.78-SR1-20160915123031.zip

Hash verifying file transfer:
627c4b98e7bf83293e81d3758accf753 = Local Hash
627c4b98e7bf83293e81d3758accf753 = Device hash
 + Verified!

Pushing "busybox-signed.zip" to your device:

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\busybox-signed.zip" "/sdcard/!ReadyToFlash/Root_Files/busybox-signed.zip"

100%  /sdcard/!ReadyToFlash/Root_Files/busybox-signed.zip

Hash verifying file transfer:
0ece645c3ca95a10f9a4344300ce0f8f = Local Hash
0ece645c3ca95a10f9a4344300ce0f8f = Device hash
 + Verified!

Pushing "quick-reboot-signed.zip" to your device:

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\quick-reboot-signed.zip" "/sdcard/!ReadyToFlash/Root_Files/quick-reboot-signed.zip"

100%  /sdcard/!ReadyToFlash/Root_Files/quick-reboot-signed.zip

Hash verifying file transfer:
64384a4285d14f0727ea989c17c8909b = Local Hash
64384a4285d14f0727ea989c17c8909b = Device hash
 + Verified!

Pushing "openrecoveryscript" to your device:

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\openrecoveryscript" "/cache/recovery/openrecoveryscript"

100%  /cache/recovery/openrecoveryscript

Hash verifying file transfer:
b42ecaae4b4c4d37d3200b874e29366b = Local Hash
b42ecaae4b4c4d37d3200b874e29366b = Device hash
 + Verified!

Rebooting your device into bootloader mode...
adb reboot bootloader

Checking Fastboot Connectivity
fastboot devices
ENU5T15B05003467    fastboot
 + Fastboot Device Connected

Temporarily Booting TWRP...
fastboot boot "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Recovery_Custom\TWRP\twrp-3.0.2-2-angler.img"

Rooting...
Waiting for your device...
Device Detected
Automated Rooting Procedure Complete!

But when I open SuperSU app it says "Root undetected". Root Checker Basic app also cannot confirm that my phone has been rooted.

I could see the custom TWRP recovery in the rooting process, but after rooting I'm unable to open it myself, when I go to Recovery I see stock Recovery (which doesn't have options such as full factory reset, wipe cache, dalvik cache and wipe data/factory reset).

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