Rebase button times out and fails most of the time

Summary

After upgrading to 11.6, for **one ** project the rebase button times out and fails most of the time.

Steps to reproduce

Click on the Rebase button in GitLab

What is the current bug behavior?

"Rebase in progress" is shown for about 30 minutes, then rebase fails.

What is the expected correct behavior?

Rebase succeeds

Relevant logs and/or screenshots

githost.log

January 23, 2019 09:45 -> INFO -> MergeRequests::RebaseService info (root/myproject!2478): rebase started
January 23, 2019 09:45 -> INFO -> MergeRequests::RebaseService info (root/myproject!2478): rebased to 0ea026cc568c82f73b2b0770ed449c203cc85871
January 23, 2019 09:45 -> INFO -> MergeRequests::RebaseService info (root/myproject!2478): rebase SHA saved: 0ea026cc568c82f73b2b0770ed449c203cc85871
January 23, 2019 10:31 -> INFO -> MergeRequests::RebaseService info (root/myproject!2479): rebase started
January 23, 2019 10:45 -> ERROR -> MergeRequests::RebaseService error (root/myproject!2479): Rebase failed. Please rebase locally
January 23, 2019 10:45 -> ERROR -> MergeRequests::RebaseService error (root/myproject!2479): 14:transport is closing
January 23, 2019 12:16 -> INFO -> MergeRequests::RebaseService info (root/myproject!2486): rebase started
January 23, 2019 12:42 -> ERROR -> MergeRequests::RebaseService error (root/myproject!2486): Rebase failed. Please rebase locally
January 23, 2019 12:42 -> ERROR -> MergeRequests::RebaseService error (root/myproject!2486): 14:transport is closing

Results of GitLab environment info

Expand for output related to GitLab environment info 
System information
System:
Proxy:          no
Current User:   git
Using RVM:      no
Ruby Version:   2.5.3p105
Gem Version:    2.7.6
Bundler Version:1.16.6
Rake Version:   12.3.1
Redis Version:  3.2.12
Git Version:    2.18.1
Sidekiq Version:5.2.3
Go Version:     unknown

GitLab information
Version:        11.6.3-ee
Revision:       76c33c6
Directory:      /opt/gitlab/embedded/service/gitlab-rails
DB Adapter:     postgresql
DB Version:     9.6.11
URL:            http://srvottodrepo01.rossvideo.com
HTTP Clone URL: http://srvottodrepo01.rossvideo.com/some-group/some-project.git
SSH Clone URL:  git@srvottodrepo01.rossvideo.com:some-group/some-project.git
Elasticsearch:  no
Geo:            no
Using LDAP:     no
Using Omniauth: yes
Omniauth Providers:


GitLab Shell
Version:        8.4.3
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 subtasks ...


Checking GitLab Shell ...


GitLab Shell: ... GitLab Shell version >= 8.4.3 ? ... OK (8.4.3)
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: ...
1/2 ... yes
1/4 ... yes
1/5 ... yes
28/6 ... yes
29/7 ... yes
28/8 ... yes
7/9 ... yes
6/10 ... yes
1/13 ... yes
41/18 ... yes
41/19 ... yes
38/21 ... yes
28/22 ... yes
42/23 ... yes
44/24 ... yes
28/26 ... yes
29/28 ... yes
51/30 ... yes
1/31 ... yes
42/32 ... yes
38/33 ... yes
57/34 ... yes
38/35 ... yes
28/36 ... yes
61/37 ... yes
61/38 ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.3.5 ? ... yes (2.5.3)
Git version >= 2.18.0 ? ... yes (2.18.1)
Git user has default SSH configuration? ... no
Try fixing it:
mkdir ~/gitlab-check-backup-1548264876
sudo mv /var/opt/gitlab/.ssh/id_rsa ~/gitlab-check-backup-1548264876
sudo mv /var/opt/gitlab/.ssh/id_rsa.pub ~/gitlab-check-backup-1548264876
For more information see:
doc/ssh/README.md in section "SSH on the GitLab server"
Please fix the error above and rerun the checks.
Active users: ... 36
Elasticsearch version 5.6 - 6.x? ... skipped (elasticsearch is disabled)


Checking GitLab App ... Finished


Checking GitLab subtasks ... Finished
Edited by C