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Help Nexus 5 stuck in the start up screen

If your system and recovery partitions are causing the problems, a factory reset won't fix it. You'll need to flash the factory firmware.

Follow these instructions and you should be fine.

That thread might have older versions of the firmware linked so go here to get the latest.
 
I would recommend using flash-all script for Android 6 preview firmware or, if you can get TWRP to work, flash the latest CyanogenMod 12.1 nightly or you can look for a TWRP flashable 6.0 PV2. Lollipop seems to have some issues upgrading from KitKat...
 
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When I flashed 6.0, the flash-all did not work for me. Instead, I had to unzip the file and manually flash each module.
 
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