'git fetch' command failed: EOFException

We have TeamCity running against a Gitea git server behind a reverse proxy. After a while we receive the following message preventing any builds from starting for that particular build configuration even though it had build successfully earlier.

I have added the PKI SSL certificate to the trust store and it does work (because it had built earlier), but eventually all build configurations stop working.

What does seem to work is to clear the TeamCity data directory git cache, then restart teamcity. It does therefore not seem like a git server problem to me.

Stack trace:

[2019-11-11 08:10:25,052] WARN [al executor 661] - cs.ConnectionStateReporterImpl - Unable to collect changes for [Libraries / [project] / [buildconfig] - Entity Framework 6.x {id=Libraries_[name]_[name]EntityFramework6x, internal id=bt21}]: jetbrains.buildServer.vcs.VcsRootVcsException: Error collecting changes for VCS repository '"library.[name].git" {instance id=585, parent internal id=8, parent id=Libraries_[name]_LibraryGit1, description: "https://git.[domain]/libraries/[name].git#refs/heads/entity-framework"}'
'git fetch' command failed (repository dir: <TeamCity data dir>/system/caches/git/git-D065B5B8.git).
stderr: Error while pruning removed branches: java.io.EOFException
java.lang.RuntimeException: java.io.EOFException
at jetbrains.buildServer.util.ssl.SSLContextUtil.getDefaultTrustStore(SSLContextUtil.java:138)
at jetbrains.buildServer.util.ssl.SSLContextUtil.createUserSSLContext(SSLContextUtil.java:51)
at jetbrains.buildServer.buildTriggers.vcs.git.SSLHttpClientConnection.getSSLContext(SSLHttpClientConnection.java:155)
at jetbrains.buildServer.buildTriggers.vcs.git.SSLHttpClientConnection.configure(SSLHttpClientConnection.java:381)
at org.eclipse.jgit.transport.TransportHttp.disableSslVerify(TransportHttp.java:579)
at org.eclipse.jgit.transport.TransportHttp.httpOpen(TransportHttp.java:553)
at org.eclipse.jgit.transport.TransportHttp.httpOpen(TransportHttp.java:535)
at org.eclipse.jgit.transport.TransportHttp.connect(TransportHttp.java:474)
at org.eclipse.jgit.transport.TransportHttp.openFetch(TransportHttp.java:315)
at jetbrains.buildServer.buildTriggers.vcs.git.GitServerUtil.pruneRemovedBranches(GitServerUtil.java:362)
at jetbrains.buildServer.buildTriggers.vcs.git.GitServerUtil.pruneRemovedBranches(GitServerUtil.java:346)
at jetbrains.buildServer.buildTriggers.vcs.git.Fetcher.pruneRemovedBranches(Fetcher.java:131)
at jetbrains.buildServer.buildTriggers.vcs.git.Fetcher.fetch(Fetcher.java:110)
at jetbrains.buildServer.buildTriggers.vcs.git.Fetcher.main(Fetcher.java:64)
Caused by: java.io.EOFException
at java.io.DataInputStream.readInt(DataInputStream.java:392)
at sun.security.provider.JavaKeyStore.engineLoad(JavaKeyStore.java:658)
at sun.security.provider.JavaKeyStore$JKS.engineLoad(JavaKeyStore.java:56)
at sun.security.provider.KeyStoreDelegator.engineLoad(KeyStoreDelegator.java:224)
at sun.security.provider.JavaKeyStore$DualFormatJKS.engineLoad(JavaKeyStore.java:70)
at java.security.KeyStore.load(KeyStore.java:1445)
at jetbrains.buildServer.util.ssl.SSLContextUtil.getStore(SSLContextUtil.java:158)
at jetbrains.buildServer.util.ssl.SSLContextUtil.getDefaultTrustStore(SSLContextUtil.java:132)
... 13 more
java.io.EOFException
exit code: 1: jetbrains.buildServer.vcs.VcsRootVcsException: Error collecting changes for VCS repository '"library.[name].git" {instance id=585, parent internal id=8, parent id=Libraries_[name]_LibraryGit1, description: "https://git.[domain]/libraries/[name].git#refs/heads/entity-framework"}'
'git fetch' command failed (repository dir: <TeamCity data dir>/system/caches/git/git-D065B5B8.git).
stderr: Error while pruning removed branches: java.io.EOFException
java.lang.RuntimeException: java.io.EOFException
at jetbrains.buildServer.util.ssl.SSLContextUtil.getDefaultTrustStore(SSLContextUtil.java:138)
at jetbrains.buildServer.util.ssl.SSLContextUtil.createUserSSLContext(SSLContextUtil.java:51)
at jetbrains.buildServer.buildTriggers.vcs.git.SSLHttpClientConnection.getSSLContext(SSLHttpClientConnection.java:155)
at jetbrains.buildServer.buildTriggers.vcs.git.SSLHttpClientConnection.configure(SSLHttpClientConnection.java:381)
at org.eclipse.jgit.transport.TransportHttp.disableSslVerify(TransportHttp.java:579)
at org.eclipse.jgit.transport.TransportHttp.httpOpen(TransportHttp.java:553)
at org.eclipse.jgit.transport.TransportHttp.httpOpen(TransportHttp.java:535)
at org.eclipse.jgit.transport.TransportHttp.connect(TransportHttp.java:474)
at org.eclipse.jgit.transport.TransportHttp.openFetch(TransportHttp.java:315)
at jetbrains.buildServer.buildTriggers.vcs.git.GitServerUtil.pruneRemovedBranches(GitServerUtil.java:362)
at jetbrains.buildServer.buildTriggers.vcs.git.GitServerUtil.pruneRemovedBranches(GitServerUtil.java:346)
at jetbrains.buildServer.buildTriggers.vcs.git.Fetcher.pruneRemovedBranches(Fetcher.java:131)
at jetbrains.buildServer.buildTriggers.vcs.git.Fetcher.fetch(Fetcher.java:110)
at jetbrains.buildServer.buildTriggers.vcs.git.Fetcher.main(Fetcher.java:64)
Caused by: java.io.EOFException
at java.io.DataInputStream.readInt(DataInputStream.java:392)
at sun.security.provider.JavaKeyStore.engineLoad(JavaKeyStore.java:658)
at sun.security.provider.JavaKeyStore$JKS.engineLoad(JavaKeyStore.java:56)
at sun.security.provider.KeyStoreDelegator.engineLoad(KeyStoreDelegator.java:224)
at sun.security.provider.JavaKeyStore$DualFormatJKS.engineLoad(JavaKeyStore.java:70)
at java.security.KeyStore.load(KeyStore.java:1445)
at jetbrains.buildServer.util.ssl.SSLContextUtil.getStore(SSLContextUtil.java:158)
at jetbrains.buildServer.util.ssl.SSLContextUtil.getDefaultTrustStore(SSLContextUtil.java:132)
... 13 more
java.io.EOFException
exit code: 1 (enable debug to see stacktrace)