Git prompt for a password despite of passing all checks related with ssh key

Summary

git prompts for a password despite set ssh key properly and pass all checks. I added the key following generating-a-new-ssh-key-pair.

Steps to reproduce

I installed gitlab-ce using apt-get and make it works for localhost. Nginx serves it through proxy. I migrated database from old version. I do not remember specific version of previous version I used but gitlab works properly except for this issue. And SSH server is working at 8080 port.

What is the current bug behavior?

git prompts for a password.

What is the expected correct behavior?

git works without prompting for a password.

Relevant logs and/or screenshots

$ git remote -v
origin	https://gitlab.example.com/some-group/some-project.git (fetch)
origin	https://gitlab.example.com/some-group/some-project.git (push)
$ git fetch
Username for 'https://gitlab.example.com':
$ sudo gitlab-rake gitlab:check SANITIZE=true
...
Git user has default SSH configuration? ... yes
...
$ sudo /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
$ sudo tail /var/log/gitlab/gitlab-shell/gitlab-shell.log
...
I, [2017-10-20T03:06:45.248906 #30787]  INFO -- : Adding key key-19 => "ssh-rsa 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"
...
$ sudo cat /etc/gitlab/gitlab.rb
...
external_url 'https://gitlab.example.com'
...
nginx['redirect_http_to_https'] = false
nginx['listen_addresses'] = ['127.0.0.1']
nginx['listen_port'] = 8000
nginx['listen_https'] = false
nginx['proxy_set_headers'] = {
  "X-Forwarded-Proto" => "https",
  "X-Forwarded-Ssl" => "on",
}
$ sudo cat /etc/nginx/site-available/gitlab
server {
    listen 80 default_server;
    listen [::]:80 default_server;

    server_name gitlab.example.com;

    location / {
        return 301 https://$server_name$request_uri;
    }
}

server {
    listen 443 ssl http2 default_server;
    listen [::]:443 ssl http2 default_server;

    server_name gitlab.example.com;

    # here is ssl settings...

    location / {
        proxy_redirect          off;
        proxy_set_header        Host $http_host;
        proxy_set_header        X-Real-IP $remote_addr;
        proxy_set_header        X-Forwarded-Proto $scheme;
        proxy_set_header        X-Forwarded-For $proxy_add_x_forwarded_for;

        proxy_read_timeout      300;
        proxy_connect_timeout   300;

        proxy_pass              http://localhost:8000;
    }
}

Output of checks

Results of GitLab environment info

Expand for output related to GitLab environment info 
System information
System:		Ubuntu 16.04
Current User:	git
Using RVM:	no
Ruby Version:	2.3.5p376
Gem Version:	2.6.13
Bundler Version:1.13.7
Rake Version:	12.0.0
Redis Version:	3.2.5
Git Version:	2.13.5
Sidekiq Version:5.0.4
Go Version:	unknown

GitLab information
Version:	10.0.3
Revision:	8895150
Directory:	/opt/gitlab/embedded/service/gitlab-rails
DB Adapter:	postgresql
URL:		https://gitlab.example.com
HTTP Clone URL:	https://gitlab.example.com/some-group/some-project.git
SSH Clone URL:	git@gitlab.example.com:some-group/some-project.git
Using LDAP:	no
Using Omniauth:	no


GitLab Shell
Version:	5.9.0
Repository storage paths:
  • default: /var/opt/gitlab/git-data/repositories Hooks: /opt/gitlab/embedded/service/gitlab-shell/hooks Git: /opt/gitlab/embedded/bin/git

Results of GitLab application Check

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

GitLab Shell version >= 5.9.0 ? ... OK (5.9.0)
Repo base directory exists?
default... yes
Repo storage directories are symlinks?
default... no
Repo paths owned by git:root, or git:git?
default... yes
Repo paths access is drwxrws---?
default... yes
hooks directories in repos are links: ...
16/2 ... ok
13/3 ... ok
3/5 ... ok
46/10 ... repository is empty
53/11 ... ok
53/12 ... ok
54/16 ... ok
13/18 ... ok
16/20 ... ok
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 Sidekiq ...


Running? ... yes
Number of Sidekiq processes ... 1


Checking Sidekiq ... Finished


Reply by email is disabled in config/gitlab.yml
Checking LDAP ...


LDAP is disabled in config/gitlab.yml


Checking LDAP ... Finished


Checking GitLab ...


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: ...
16/2 ... yes
13/3 ... yes
3/5 ... yes
46/10 ... yes
53/11 ... yes
53/12 ... yes
54/16 ... yes
13/18 ... yes
16/20 ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.3.3 ? ... yes (2.3.5)
Git version >= 2.7.3 ? ... yes (2.13.5)
Git user has default SSH configuration? ... yes
Active users: ... 55


Checking GitLab ... Finished
Edited by Junsang Cheon