This article covers some of the issues you may experience when using GnuPG (GPG) with your YubiKey and possible solutions.
GPG Does Not See the YubiKey
If you run gpg --card-status with the YubiKey plugged in and GPG does not detect the YubiKey, try the steps below.
Your device does not support the OpenPGP applet. See the Applicable Products section above.
Using YubiKey Manager, verify that your YubiKey has CCID enabled and the OpenPGP application installed. If CCID is disabled, you can use YubiKey Manager to enable it.
Specify the smart card reader GPG uses by adding the line “reader-port Yubico Yubikey” (without quotes) to the scdaemon.conf file; create the file if it does not exist. After making this change, reboot your computer to ensure it takes affect.
On Windows the file is located at: %APPDATA%\gnupg\scdaemon.conf
On macOS and Linux it is at: ~/.gnupg/scdaemon.conf
Importing PGP Key to the YubiKey Fails
If you run keytocard under the gpg --card-edit feature and it fails, this usually indicates you are using a large key (4096bit) and an older version of GPG. For large keys you need to use GPG v2.0 or newer which you can verify by running gpg --version. On some systems, both GPG v1.x and GPG v2.x exist simultaneously and you need to access GPG v2 by running gpg2 instead of gpg.