Permission denied with local runner

Hello everybody,

I have been using an already installed GitLab via Intellij on my own server for several months.
Everything went perfectly. After an update of the server operating system, however, the runner doesnt worked and I had to install a local runner.
This now runs as a docker. However, the deployment no longer works. GitLab reports:

 Running with gitlab-runner 12.8.0 (1b659122)
   on test_deploy PxtTQG1j
Using Shell executor...
Running on 32723a6da6bb...
Fetching changes...
 Initialized empty Git repository in /home/gitlab-runner/builds/PxtTQG1j/0/MyProject/.git/
 Created fresh repository.
 From https://gitlab........

 Checking out c04bf48f as development...
 Skipping object checkout, Git LFS is not installed.
 Skipping Git submodules setup
$ which dot || ( apt-get update -y && apt-get install graphviz -y )
 Reading package lists...
 E: List directory /var/lib/apt/lists/partial is missing. - Acquire (13: Permission denied)
 ERROR: Job failed: exit status 1

Unfortunately I don’t know what to do to make it work.
Does anyone have a hint to solve this problem?

Thanks in advance,