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I am trying to update the guppy_basecaller (current version installed is 3.2.10+aabd4ec) on a ONT Gridion device. I am initially trying to update it via the nanopore PPA, as described here (requires login access to the nanopore community)

After I issued sudo apt update, I got a GPG error, saying that the public key was not found in the system.

W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://europe.oxfordnanoportal.com/apt xenial-stable InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY AD9D09AF2EBBA5A8
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://mirror.oxfordnanoportal.com/apt xenial-stable-gridion InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY AD9D09AF2EBBA5A8
W: Failed to fetch https://mirror.oxfordnanoportal.com/apt/dists/xenial-stable-gridion/InRelease  The following signatures couldn't be verified because the public key is not available: NO_PUBKEY AD9D09AF2EBBA5A8
W: Failed to fetch http://mirror.oxfordnanoportal.com/apt/dists/xenial-stable/InRelease  The following signatures couldn't be verified because the public key is not available: NO_PUBKEY AD9D09AF2EBBA5A8
W: Some index files failed to download. They have been ignored, or old ones used instead

I came across a possible solution shown here, so I tried to add the key to the system with the following command:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys AD9D09AF2EBBA5A8

The terminal was busy for too long and, after some time I got an timeout error:

Executing: /tmp/tmp.EWnOg4cPJk/gpg.1.sh --keyserver
keyserver.ubuntu.com
--recv-keys
AD9D09AF2EBBA5A8
gpg: requesting key 2EBBA5A8 from hkp server keyserver.ubuntu.com
gpg: keyserver timed out
gpg: keyserver receive failed: keyserver error

I then came across this post where one potential solution was to change the port, so I issued:

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys AD9D09AF2EBBA5A8

But then I got:

Executing: /tmp/tmp.sfqFuJpVb2/gpg.1.sh --keyserver
hkp://keyserver.ubuntu.com:80
--recv-keys
AD9D09AF2EBBA5A8
gpg: requesting key 2EBBA5A8 from hkp server keyserver.ubuntu.com
gpgkeys: key AD9D09AF2EBBA5A8 not found on keyserver
gpg: no valid OpenPGP data found.
gpg: Total number processed: 0
gpg: keyserver communications error: key not found
gpg: keyserver communications error: bad public key
gpg: keyserver receive failed: bad public key

Has anyone managed to update the guppy_basecaller via PPA, as described in the nanopore community page?

An alternative would be to install via the .tar.gz file, though I am first trying to upgrade the current version from the PPA to avoid conflicts with the current installation.

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This is an ONT problem, not an ubuntu problem. Keys can expire over time, and need to be updated.

The keys for the Guppy basecaller are not present in the ubuntu repository; you need to get them from ONT. This is indicated by the installation instructions for Guppy (which you've already linked to):

sudo apt-get update
sudo apt-get install wget lsb-release
export PLATFORM=$(lsb_release -cs)
###
wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add -
###
echo "deb http://mirror.oxfordnanoportal.com/apt ${PLATFORM}-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list
sudo apt-get update
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  • $\begingroup$ Yes it turned out that the upgrade worked after repeating all these commands (which I thought it was not necessary because I had already added the PPA). There was, however, an issue with the release, so export PLATFORM=$(lsb_release -cs) fixed the issue $\endgroup$
    – BCArg
    Feb 25 at 14:28

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