likely caused by
https://github.com/jenkinsci/jenkins/pull/6025
I've hit this twice recently with the core-pr-tester
I assume two things are trying to load the update center data at the same time before the updates directory exists.
1 time plugin data wasn't available and the other time it did load.
This may also be found at: /root/.jenkins/secrets/initialAdminPassword
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2022-01-18 08:25:54.927+0000 [id=35] WARNING hudson.model.UpdateCenter#updateDefaultSite: Upgrading Jenkins. Failed to update the default Update Site 'default'. Plugin upgrades may fail.
java.nio.file.FileAlreadyExistsException: /root/.jenkins/updates
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:94)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
at java.base/sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:389)
at java.base/java.nio.file.Files.createDirectory(Files.java:690)
at hudson.Util.createDirectories(Util.java:1785)
at hudson.util.TextFile.write(TextFile.java:100)
at hudson.model.UpdateSite.updateData(UpdateSite.java:248)
at hudson.model.UpdateSite.updateDirectlyNow(UpdateSite.java:219)
at hudson.model.UpdateSite.updateDirectlyNow(UpdateSite.java:214)
at hudson.model.UpdateCenter.updateDefaultSite(UpdateCenter.java:2667)
at jenkins.install.SetupWizard.init(SetupWizard.java:206)
at jenkins.install.InstallState$InitialSecuritySetup.initializeState(InstallState.java:182)
at jenkins.model.Jenkins.setInstallState(Jenkins.java:1129)
at jenkins.install.InstallUtil.proceedToNextStateFrom(InstallUtil.java:98)
at jenkins.install.InstallState$Unknown.initializeState(InstallState.java:88)
at jenkins.model.Jenkins$15.run(Jenkins.java:3491)
at org.jvnet.hudson.reactor.TaskGraphBuilder$TaskImpl.run(TaskGraphBuilder.java:175)
at org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:305)
at jenkins.model.Jenkins$5.runTask(Jenkins.java:1156)
at org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:222)
at org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:121)
at jenkins.security.ImpersonatingExecutorService$1.run(ImpersonatingExecutorService.java:68)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)