Some existing project started returning 404s, but they're still on the filesystem

Summary

We discovered yesterday that we get 404s accessing some projects on our Gitlab instance although the repositories weren’t deleted and they’re still present on the filesystem and don’t seem to have issues, git fsck ran without issues. git pull also returns > GitLab: The project you were looking for could not be found..

What is the current bug behavior?

Accessing existing non-deleted projects returns a 404 not found page and git pull returns:

> GitLab: The project you were looking for could not be found.
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

Relevant logs and/or screenshots

`gitlab-tail` while GET'ing the project's web page

==> /var/log/gitlab/gitlab-rails/production_json.log <==
{"method":"GET","path":"/software/hubdroid-web","format":"html","controller":"ApplicationController","action":"route_not_found","status":404,"duration":45.28,"view":19.39,"db":3.59,"time":"2019-08-06T20:30:54.761Z","params":[{"key":"unmatched_route","value":"software/hubdroid-web"}],"remote_ip":"199.167.106.19","user_id":2,"username":"alf","ua":"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/75.0.3770.100 Safari/537.36","queue_duration":null,"correlation_id":"gMPoxvKRhZ1"}

==> /var/log/gitlab/gitlab-rails/production.log <==
Started GET "/software/hubdroid-web" for 199.167.106.19 at 2019-08-06 20:30:54 +0000
Processing by ApplicationController#route_not_found as HTML
  Parameters: {"unmatched_route"=>"software/hubdroid-web"}
Completed 404 Not Found in 45ms (Views: 19.4ms | ActiveRecord: 3.6ms)

==> /var/log/gitlab/nginx/gitlab_access.log <==
199.167.106.19 - - [06/Aug/2019:20:30:54 +0000] "GET /software/hubdroid-web HTTP/2.0" 404 6301 "" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/75.0.3770.100 Safari/537.36"

==> /var/log/gitlab/gitlab-workhorse/current <==
{"correlation_id":"gMPoxvKRhZ1","duration":0.073678062,"host":"git.pixmob.com","level":"info","method":"GET","msg":"access","proto":"HTTP/1.1","referer":"","remoteAddr":"199.167.106.19:0","remoteIp":"199.167.106.19","status":404,"system":"http","time":"2019-08-06T20:30:54Z","uri":"/software/hubdroid-web","userAgent":"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/75.0.3770.100 Safari/537.36","written":29553}
`gitlab-tail` while doing a `git pull`

==> /var/log/gitlab/gitlab-rails/api_json.log <==
{"time":"2019-08-06T20:37:59.228Z","severity":"INFO","duration":15.09,"db":6.15,"view":8.94,"status":404,"method":"POST","path":"/api/v4/internal/allowed","params":[{"key":"action","value":"git-upload-pack"},{"key":"changes","value":"_any"},{"key":"gl_repository","value":null},{"key":"project","value":"software/hub-lib.git"},{"key":"protocol","value":"ssh"},{"key":"env","value":"{}"},{"key":"key_id","value":"1"},{"key":"secret_token","value":"[FILTERED]"}],"host":"127.0.0.1","ip":"127.0.0.1","ua":"Ruby","route":"/api/:version/internal/allowed","gitaly_calls":0,"gitaly_duration":0,"correlation_id":"26b719ea-f4dd-411d-b15b-c2d3163aefe8"}

==> /var/log/gitlab/gitlab-rails/production.log <==
Started POST "/api/v4/internal/allowed" for 127.0.0.1 at 2019-08-06 20:37:59 +0000

==> /var/log/gitlab/gitlab-shell/gitlab-shell.log <==
{"method":"POST","url":"http://127.0.0.1:8080/api/v4/internal/allowed","duration":0.039637387,"gitaly_embedded":false,"pid":29952,"level":"info","msg":"finished HTTP request","time":"2019-08-06T20:37:59+00:00"}
{"method":"POST","url":"http://127.0.0.1:8080/api/v4/internal/allowed","code":"404","body":"{\"status\":false,\"message\":\"The project you were looking for could not be found.\"}","pid":29952,"level":"error","msg":"Call failed","time":"2019-08-06T20:37:59+00:00"}
{"command":"git-upload-pack 'software/hub-lib.git'","user":"user with id key-1","pid":29952,"level":"warn","msg":"Access denied","time":"2019-08-06T20:37:59+00:00"}
`gitlab-tail` while doing a `git push`

==> /var/log/gitlab/gitlab-rails/production_json.log <==
{"method":"POST","path":"/api/v4/internal/allowed","format":"*/*","controller":"Gitlab::RequestForgeryProtection::Controller","action":"index","status":422,"error":"ActionController::InvalidAuthenticityToken: ActionController::InvalidAuthenticityToken","duration":1.1,"view":0.0,"db":0.0,"time":"2019-08-06T20:40:17.739Z","params":[{"key":"changes","value":"_any"},{"key":"gl_repository","value":null},{"key":"project","value":"software/hub-lib.git"},{"key":"protocol","value":"ssh"},{"key":"env","value":"{}"},{"key":"key_id","value":"1"},{"key":"secret_token","value":"[FILTERED]"}],"remote_ip":null,"user_id":null,"username":null,"ua":null,"queue_duration":null,"correlation_id":"965e8935-715d-482d-8e5b-24f6455b4f67"}

==> /var/log/gitlab/gitlab-rails/api_json.log <==
{"time":"2019-08-06T20:40:17.741Z","severity":"INFO","duration":80.09,"db":29.85,"view":50.24,"status":500,"method":"POST","path":"/api/v4/internal/allowed","params":[{"key":"action","value":"git-receive-pack"},{"key":"changes","value":"_any"},{"key":"gl_repository","value":null},{"key":"project","value":"software/hub-lib.git"},{"key":"protocol","value":"ssh"},{"key":"env","value":"{}"},{"key":"key_id","value":"1"},{"key":"secret_token","value":"[FILTERED]"}],"host":"127.0.0.1","ip":"127.0.0.1","ua":"Ruby","route":"/api/:version/internal/allowed","gitaly_calls":0,"gitaly_duration":0,"correlation_id":"965e8935-715d-482d-8e5b-24f6455b4f67"}

==> /var/log/gitlab/gitlab-rails/production.log <==
Started POST "/api/v4/internal/allowed" for 127.0.0.1 at 2019-08-06 20:40:17 +0000
Unable to save project. Error: Name has already been taken
Processing by Gitlab::RequestForgeryProtection::Controller#index as */*
  Parameters: {"changes"=>"_any", "gl_repository"=>nil, "project"=>"software/hub-lib.git", "protocol"=>"ssh", "env"=>"{}", "key_id"=>"1", "secret_token"=>"[FILTERED]"}
Can't verify CSRF token authenticity.
This CSRF token verification failure is handled internally by `GitLab::RequestForgeryProtection`
Unlike the logs may suggest, this does not result in an actual 422 response to the user
For API requests, the only effect is that `current_user` will be `nil` for the duration of the request
Completed 422 Unprocessable Entity in 1ms (ActiveRecord: 0.0ms)

Gitlab::GitAccess::ProjectCreationError (Could not create project: Name has already been taken):
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git_access.rb:226:in `ensure_project_on_push!'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/git_access.rb:75:in `check'
  /opt/gitlab/embedded/service/gitlab-rails/lib/api/internal.rb:69:in `block (2 levels) in '
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/endpoint.rb:57:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/endpoint.rb:57:in `block (2 levels) in generate_api_method'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/activesupport-5.2.3/lib/active_support/notifications.rb:170:in `instrument'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/endpoint.rb:56:in `block in generate_api_method'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/endpoint.rb:262:in `block in run'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/activesupport-5.2.3/lib/active_support/notifications.rb:170:in `instrument'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/endpoint.rb:243:in `run'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/endpoint.rb:313:in `block in build_stack'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/middleware/base.rb:31:in `call!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/middleware/base.rb:24:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/middleware/base.rb:31:in `call!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/middleware/base.rb:24:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-oauth2-1.9.3/lib/rack/oauth2/server/resource.rb:20:in `_call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-oauth2-1.9.3/lib/rack/oauth2/server/resource/bearer.rb:8:in `_call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-oauth2-1.9.3/lib/rack/oauth2/server/abstract/handler.rb:17:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/middleware/error.rb:38:in `block in call!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/middleware/error.rb:37:in `catch'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/middleware/error.rb:37:in `call!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/middleware/base.rb:24:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape_logging-1.7.0/lib/grape_logging/middleware/request_logger.rb:60:in `block in call!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape_logging-1.7.0/lib/grape_logging/middleware/request_logger.rb:58:in `catch'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape_logging-1.7.0/lib/grape_logging/middleware/request_logger.rb:58:in `call!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/middleware/base.rb:24:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/head.rb:12:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/endpoint.rb:227:in `call!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/endpoint.rb:221:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/router/route.rb:72:in `exec'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/router.rb:121:in `process_route'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/router.rb:74:in `block in identity'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/router.rb:93:in `transaction'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/router.rb:72:in `identity'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/router.rb:57:in `block in call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/router.rb:137:in `with_optimization'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/router.rb:56:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/api.rb:119:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/api.rb:45:in `call!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/grape-1.1.0/lib/grape/api.rb:40:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/routing/mapper.rb:19:in `block in '
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/routing/mapper.rb:48:in `serve'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/journey/router.rb:52:in `block in serve'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/journey/router.rb:35:in `each'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/journey/router.rb:35:in `serve'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/routing/route_set.rb:840:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/omniauth-1.9.0/lib/omniauth/strategy.rb:420:in `call_app!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/omniauth-saml-1.10.0/lib/omniauth/strategies/saml.rb:86:in `other_phase'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/omniauth-1.9.0/lib/omniauth/strategy.rb:190:in `call!'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/omniauth-1.9.0/lib/omniauth/strategy.rb:169:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/multipart.rb:103:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/request_profiler/middleware.rb:16:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/go.rb:20:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/etag_caching/middleware.rb:13:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/correlation_id.rb:16:in `block in call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/gitlab-labkit-0.3.0/lib/labkit/correlation/correlation_id.rb:18:in `use_id'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/correlation_id.rb:15:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/batch-loader-1.4.0/lib/batch_loader/middleware.rb:11:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/apollo_upload_server-2.0.0.beta.3/lib/apollo_upload_server/middleware.rb:20:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-attack-4.4.1/lib/rack/attack.rb:107:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/warden-1.2.7/lib/warden/manager.rb:36:in `block in call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/warden-1.2.7/lib/warden/manager.rb:35:in `catch'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/warden-1.2.7/lib/warden/manager.rb:35:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-cors-1.0.2/lib/rack/cors.rb:97:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/tempfile_reaper.rb:15:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/etag.rb:25:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/conditional_get.rb:38:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/head.rb:12:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/http/content_security_policy.rb:18:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/read_only/controller.rb:40:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/read_only.rb:18:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/session/abstract/id.rb:232:in `context'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/session/abstract/id.rb:226:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/middleware/cookies.rb:670:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/middleware/callbacks.rb:28:in `block in call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/activesupport-5.2.3/lib/active_support/callbacks.rb:98:in `run_callbacks'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/middleware/callbacks.rb:26:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/middleware/debug_exceptions.rb:61:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/middleware/show_exceptions.rb:33:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/basic_health_check.rb:25:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/railties-5.2.3/lib/rails/rack/logger.rb:38:in `call_app'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/railties-5.2.3/lib/rails/rack/logger.rb:26:in `block in call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/activesupport-5.2.3/lib/active_support/tagged_logging.rb:71:in `block in tagged'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/activesupport-5.2.3/lib/active_support/tagged_logging.rb:28:in `tagged'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/activesupport-5.2.3/lib/active_support/tagged_logging.rb:71:in `tagged'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/railties-5.2.3/lib/rails/rack/logger.rb:26:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/middleware/remote_ip.rb:81:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/request_context.rb:26:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/request_store-1.3.1/lib/request_store/middleware.rb:9:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/middleware/request_id.rb:27:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/method_override.rb:22:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/runtime.rb:22:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/actionpack-5.2.3/lib/action_dispatch/middleware/executor.rb:14:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/sendfile.rb:111:in `call'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/metrics/requests_rack_middleware.rb:29:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/sentry-raven-2.9.0/lib/raven/integrations/rack.rb:51:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/railties-5.2.3/lib/rails/engine.rb:524:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/railties-5.2.3/lib/rails/railtie.rb:190:in `public_send'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/railties-5.2.3/lib/rails/railtie.rb:190:in `method_missing'
  /opt/gitlab/embedded/service/gitlab-rails/lib/gitlab/middleware/release_env.rb:12:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/urlmap.rb:68:in `block in call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/urlmap.rb:53:in `each'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/rack-2.0.7/lib/rack/urlmap.rb:53:in `call'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/unicorn-5.4.1/lib/unicorn/http_server.rb:606:in `process_client'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/unicorn-worker-killer-0.4.4/lib/unicorn/worker_killer.rb:52:in `process_client'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/unicorn-5.4.1/lib/unicorn/http_server.rb:701:in `worker_loop'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/unicorn-5.4.1/lib/unicorn/http_server.rb:549:in `spawn_missing_workers'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/unicorn-5.4.1/lib/unicorn/http_server.rb:563:in `maintain_worker_count'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/unicorn-5.4.1/lib/unicorn/http_server.rb:293:in `join'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/unicorn-5.4.1/bin/unicorn:126:in `'
  /opt/gitlab/embedded/bin/unicorn:23:in `load'
  /opt/gitlab/embedded/bin/unicorn:23:in `'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/cli/exec.rb:74:in `load'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/cli/exec.rb:74:in `kernel_load'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/cli/exec.rb:28:in `run'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/cli.rb:463:in `exec'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/vendor/thor/lib/thor/command.rb:27:in `run'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/vendor/thor/lib/thor/invocation.rb:126:in `invoke_command'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/vendor/thor/lib/thor.rb:387:in `dispatch'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/cli.rb:27:in `dispatch'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/vendor/thor/lib/thor/base.rb:466:in `start'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/cli.rb:18:in `start'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/exe/bundle:30:in `block in '
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/lib/bundler/friendly_errors.rb:124:in `with_friendly_errors'
  /opt/gitlab/embedded/lib/ruby/gems/2.6.0/gems/bundler-1.17.3/exe/bundle:22:in `'
  /opt/gitlab/embedded/bin/bundle:23:in `load'
  /opt/gitlab/embedded/bin/bundle:23:in `'

==> /var/log/gitlab/gitlab-shell/gitlab-shell.log <==
{"method":"POST","url":"http://127.0.0.1:8080/api/v4/internal/allowed","duration":0.103407877,"gitaly_embedded":false,"pid":31105,"level":"info","msg":"finished HTTP request","time":"2019-08-06T20:40:17+00:00"}
{"method":"POST","url":"http://127.0.0.1:8080/api/v4/internal/allowed","code":"500","body":"{\"message\":\"500 Internal Server Error\"}","pid":31105,"level":"error","msg":"Call failed","time":"2019-08-06T20:40:17+00:00"}
{"command":"git-receive-pack 'software/hub-lib.git'","user":"user with id key-1","pid":31105,"level":"warn","msg":"Access denied","time":"2019-08-06T20:40:17+00:00"}
Output of routes table

gitlabhq_production=> SELECT * FROM routes WHERE path = 'software/hub-lib';
 id  | source_id | source_type |       path       |         created_at         |         updated_at         |        name
-----+-----------+-------------+------------------+----------------------------+----------------------------+--------------------
 328 |       355 | Project     | software/hub-lib | 2019-04-30 13:25:16.825741 | 2019-04-30 13:25:16.825741 | software / hub-lib
(1 row)

Output of checks

Results of GitLab environment info

Expand for output related to GitLab environment info
System information
System:		Ubuntu 18.04
Current User:	git
Using RVM:	no
Ruby Version:	2.6.3p62
Gem Version:	2.7.9
Bundler Version:1.17.3
Rake Version:	12.3.2
Redis Version:	3.2.12
Git Version:	2.21.0
Sidekiq Version:5.2.7
Go Version:	unknown

GitLab information
Version: 12.1.3
Revision: 6ccbccc2010
Directory: /opt/gitlab/embedded/service/gitlab-rails
DB Adapter: PostgreSQL
DB Version: 10.7
URL: https://git.pixmob.com
HTTP Clone URL: https://git.pixmob.com/some-group/some-project.git
SSH Clone URL: git@git.pixmob.com:some-group/some-project.git
Using LDAP: no
Using Omniauth: yes
Omniauth Providers: saml

GitLab Shell
Version: 9.3.0
Repository storage paths:

  • default: /var/opt/gitlab/git-data/repositories
    GitLab Shell path: /opt/gitlab/embedded/service/gitlab-shell
    Git: /opt/gitlab/embedded/bin/git

Results of GitLab application Check

Expand for output related to the GitLab application check
Checking GitLab subtasks ...

Checking GitLab Shell …

GitLab Shell: … GitLab Shell version >= 9.3.0 ? … OK (9.3.0)
Running /opt/gitlab/embedded/service/gitlab-shell/bin/check
Check GitLab API access: OK
Redis available via internal API: OK

Access to /var/opt/gitlab/.ssh/authorized_keys: OK
gitlab-shell self-check successful

Checking GitLab Shell … Finished

Checking Gitaly …

Gitaly: … default … OK

Checking Gitaly … Finished

Checking Sidekiq …

Sidekiq: … Running? … yes
Number of Sidekiq processes … 1

Checking Sidekiq … Finished

Checking Incoming Email …

Incoming Email: … Reply by email is disabled in config/gitlab.yml

Checking Incoming Email … Finished

Checking LDAP …

LDAP: … LDAP is disabled in config/gitlab.yml

Checking LDAP … Finished

Checking GitLab App …

Git configured correctly? … yes
Database config exists? … yes
All migrations up? … yes
Database contains orphaned GroupMembers? … no
GitLab config exists? … yes
GitLab config up to date? … yes
Log directory writable? … yes
Tmp directory writable? … yes
Uploads directory exists? … yes
Uploads directory has correct permissions? … yes
Uploads directory tmp has correct permissions? … yes
Init script exists? … skipped (omnibus-gitlab has no init script)
Init script up-to-date? … skipped (omnibus-gitlab has no init script)
Projects have namespace: …
57/2 … yes
57/3 … yes
57/9 … yes
57/10 … yes
57/12 … yes
57/13 … yes
57/15 … yes
13/17 … yes
57/18 … yes
57/19 … yes
5/28 … yes
57/29 … yes
57/36 … yes
57/41 … yes
57/42 … yes
57/45 … yes
27/51 … yes
27/52 … yes
57/68 … yes
57/77 … yes
13/79 … yes
31/82 … yes
32/83 … yes
32/84 … yes
32/85 … yes
32/86 … yes
32/87 … yes
32/88 … yes
32/89 … yes
32/90 … yes
57/91 … yes
37/114 … yes
37/115 … yes
40/116 … yes
40/117 … yes
40/118 … yes
40/119 … yes
40/120 … yes
40/121 … yes
38/138 … yes
38/139 … yes
38/140 … yes
39/143 … yes
47/144 … yes
47/145 … yes
47/147 … yes
47/149 … yes
37/150 … yes
47/151 … yes
37/153 … yes
38/154 … yes
37/155 … yes
37/157 … yes
37/158 … yes
38/162 … yes
37/163 … yes
47/165 … yes
40/167 … yes
39/168 … yes
40/170 … yes
30/175 … yes
52/176 … yes
52/177 … yes
52/178 … yes
52/179 … yes
30/181 … yes
30/182 … yes
30/183 … yes
30/184 … yes
30/186 … yes
30/187 … yes
30/188 … yes
30/189 … yes
51/190 … yes
30/191 … yes
30/192 … yes
30/193 … yes
30/194 … yes
38/195 … yes
38/196 … yes
30/197 … yes
30/198 … yes
30/199 … yes
24/200 … yes
52/201 … yes
47/204 … yes
30/205 … yes
51/206 … yes
51/207 … yes
37/208 … yes
30/209 … yes
47/210 … yes
32/211 … yes
32/212 … yes
32/213 … yes
32/214 … yes
32/215 … yes
32/216 … yes
32/217 … yes
32/218 … yes
32/219 … yes
57/220 … yes
57/221 … yes
35/222 … yes
57/224 … yes
38/226 … yes
47/229 … yes
30/231 … yes
22/232 … yes
40/233 … yes
52/235 … yes
55/237 … yes
24/240 … yes
24/243 … yes
38/245 … yes
57/246 … yes
52/248 … yes
44/250 … yes
51/251 … yes
37/252 … yes
37/253 … yes
52/254 … yes
57/257 … yes
26/258 … yes
37/264 … yes
38/266 … yes
38/267 … yes
39/268 … yes
24/269 … yes
44/270 … yes
24/271 … yes
51/272 … yes
47/273 … yes
26/274 … yes
51/275 … yes
30/276 … yes
30/277 … yes
51/278 … yes
57/279 … yes
30/280 … yes
24/281 … yes
52/282 … yes
57/283 … yes
57/284 … yes
44/285 … yes
39/287 … yes
52/288 … yes
30/290 … yes
52/291 … yes
30/292 … yes
30/293 … yes
30/294 … yes
38/296 … yes
57/298 … yes
30/299 … yes
38/301 … yes
38/302 … yes
30/303 … yes
52/304 … yes
37/305 … yes
37/306 … yes
30/307 … yes
47/308 … yes
57/309 … yes
37/310 … yes
57/311 … yes
30/313 … yes
26/314 … yes
49/315 … yes
52/317 … yes
47/318 … yes
26/319 … yes
37/320 … yes
30/321 … yes
40/322 … yes
44/323 … yes
44/324 … yes
37/325 … yes
57/326 … yes
26/327 … yes
26/328 … yes
37/329 … yes
26/330 … yes
24/331 … yes
30/332 … yes
37/333 … yes
44/334 … yes
68/335 … yes
68/336 … yes
68/337 … yes
57/338 … yes
69/345 … yes
69/346 … yes
69/347 … yes
69/348 … yes
69/350 … yes
69/351 … yes
24/352 … yes
30/353 … yes
57/354 … yes
57/355 … yes
37/356 … yes
38/357 … yes
57/358 … yes
69/359 … yes
69/360 … yes
69/361 … yes
52/362 … yes
30/363 … yes
57/364 … yes
30/365 … yes
69/367 … yes
30/368 … yes
52/369 … yes
37/371 … yes
37/372 … yes
52/373 … yes
24/378 … yes
57/380 … yes
57/381 … yes
57/382 … yes
37/383 … yes
38/384 … yes
57/385 … yes
Redis version >= 2.8.0? … yes
Ruby version >= 2.5.3 ? … yes (2.6.3)
Git version >= 2.21.0 ? … yes (2.21.0)
Git user has default SSH configuration? … yes
Active users: … 22

Checking GitLab App … Finished

Checking GitLab subtasks … Finished