A dependency to a broken submodule caused the beta-code-update-eqiad to fail.
Even removing the module afterwards did not solve the problem
On https://integration.wikimedia.org/ci/view/Beta/job/beta-code-update-eqiad/42066/console you can see the following error
00:00:50.237 Submodule path 'Wikibase': checked out 'eb1eee68a1516f9eb7ab67bb244aab689c8f3740' 00:00:51.587 Unable to checkout '54fc46411406dc3c17d8fff2ac844ebe8be637fb' in submodule path 'MathSearch' 00:00:51.588 INFO:mwextupdate:Exit code: 1
I'm afraid that this will require a manual investigation of the storage that is used by the job by an admin