the logs mysql | 2021-06-17 091348+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091348.737417Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091348.743779Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091348.743821Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091419+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091419+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql' mysql | 2021-06-17 091419+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091419+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091419.915462Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091419.916688Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091419.916797Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091448+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091448+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql' mysql | 2021-06-17 091448+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091448+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091448.916118Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091448.917661Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091448.917726Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091519+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091519+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql' mysql | 2021-06-17 091519+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091520+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091520.036442Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091520.038114Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091520.038183Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091549+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091549+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql' mysql | 2021-06-17 091549+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091549+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091549.299410Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091549.300939Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091549.301042Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091618+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091618+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql' mysql | 2021-06-17 091618+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091618+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091618.651448Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091618.653242Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091618.653469Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091650+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091650+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql' mysql | 2021-06-17 091650+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091650+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091650.468225Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091650.474352Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091650.474418Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091816+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091816+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql' mysql | 2021-06-17 091817+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091817+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091817.121322Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091817.123295Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091817.123372Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091848+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091848+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql' mysql | 2021-06-17 091848+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091848+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091848.586271Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091848.587760Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091848.587844Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091917+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091917+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql' mysql | 2021-06-17 091917+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. mysql | 2021-06-17 091917+00:00 [Note] [Entrypoint]: Initializing database files mysql | 2021-06-17T091917.967146Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). mysql | 2021-06-17T091917.970734Z 0 [ERROR] --initialize specified but the data directory has files in it. Aborting. mysql | 2021-06-17T091917.970803Z 0 [ERROR] Aborting mysql | mysql | 2021-06-17 091948+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.34-1debian10 started. Desktop (please complete the following information):

There seems to be issues in mysqldata volume. Can you try running

datahub docker nuke

and start again?

$ datahub docker nuke

Removing containers in the datahub project
Removing volumes in the datahub project
Traceback (most recent call last):
  File "/home/jill/.local/lib/python3.8/site-packages/docker/api/client.py", line 268, in _raise_for_status
    response.raise_for_status()
  File "/usr/lib/python3/dist-packages/requests/models.py", line 940, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 409 Client Error: Conflict for url: <http+docker://localhost/v1.41/volumes/datahub_mysqldata>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jill/.local/bin/datahub", line 8, in <module>
    sys.exit(main())
  File "/home/jill/.local/lib/python3.8/site-packages/datahub/entrypoints.py", line 93, in main
    sys.exit(datahub(standalone_mode=False, **kwargs))
  File "/usr/lib/python3/dist-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/jill/.local/lib/python3.8/site-packages/datahub/cli/docker.py", line 284, in nuke
    volume.remove(force=True)
  File "/home/jill/.local/lib/python3.8/site-packages/docker/models/volumes.py", line 25, in remove
    return self.client.api.remove_volume(self.id, force=force)
  File "/home/jill/.local/lib/python3.8/site-packages/docker/api/volume.py", line 161, in remove_volume
    self._raise_for_status(resp)
  File "/home/jill/.local/lib/python3.8/site-packages/docker/api/client.py", line 270, in _raise_for_status
    raise create_api_error_from_http_exception(e)
  File "/home/jill/.local/lib/python3.8/site-packages/docker/errors.py", line 31, in create_api_error_from_http_exception
    raise cls(e, response=response, explanation=explanation)
docker.errors.APIError: 409 Client Error for <http+docker://localhost/v1.41/volumes/datahub_mysqldata>: Conflict ("remove datahub_mysqldata: volume is in use - [667703d87d699a462b307fa8a9eff63042a84482f1071981a239389b596fd75b]")

do you get the same error?