Railsコマンドが効かない

何を境に起きたのかがわからないのですが、
railsコマンドを打つと以下のようなエラーを返されるようになってしまいました。
WARN箇所を確認したのですが gemfileで minitest のバージョン指定は既にしていました。
rakeがなぜ警告が出ているのかは分からないです。

ご教授お願い致します。

$rails

Beginning in Rails 4, Rails ships with a `rails` binstub at ./bin/
rails that
should be used instead of the Bundler-generated `rails` binstub.

If you are seeing this message, your binstub at ./bin/rails was ge
nerated by
Bundler instead of Rails.

You might need to regenerate your `rails` binstub locally and add
it to source
control:

 rails app:update:bin           # Bear in mind this generates othe
r binstubs
                                # too that you may or may not want
 (like yarn)

If you already have Rails binstubs in source control, you might be
inadverently overwriting them during deployment by using bundle in
stall
with the --binstubs option.

If your application was created prior to Rails 4, here's how to up
grade:

  bundle config --delete bin    # Turn off Bundler's stub generato
r
 rails app:update:bin          # Use the new Rails executables
  git add bin                   # Add bin/ to source control

You may need to remove bin/ from your .gitignore as well.

When you install a gem whose executable you want to use in your ap
p,

generate it and add it to source control:

  bundle binstubs some-gem-name
  git add bin/new-executable

WARN: Unresolved specs during Gem::Specification.reset:
      minitest (~> 5.1)
      rake (>= 0.8.7)
WARN: Clearing out unresolved specs.
Please report a bug if this causes problems.
/Library/Ruby/Gems/2.3.0/gems/bundler-1.16.5/lib/bundler/runtime.r
b:313:in `check_for_activated_spec!': You have already activated a
ctivesupport 5.2.1, but your Gemfile requires activesupport 5.1.6.
 Prepending `bundle exec` to your command may solve this. (Gem::Lo
adError)
        from /Library/Ruby/Gems/2.3.0/gems/bundler-1.16.5/lib/bund
ler/runtime.rb:31:in `block in setup'
        from /System/Library/Frameworks/Ruby.framework/Versions/2.
3/usr/lib/ruby/2.3.0/forwardable.rb:202:in `each'
        from /System/Library/Frameworks/Ruby.framework/Versions/2.
...
        from /usr/local/bin/rails:22:in `load'
        from /usr/local/bin/rails:22:in `<main>'

GemFile

source 'https://rubygems.org'

gem 'rails',        '5.1.6'
gem 'bootstrap-sass', '3.3.7'
gem 'puma',         '3.9.1'
gem 'sass-rails',   '5.0.6'
gem 'uglifier',     '3.2.0'
gem 'coffee-rails', '4.2.2'
gem 'jquery-rails', '4.3.1'
gem 'turbolinks',   '5.0.1'
gem 'jbuilder',     '2.7.0'

group :development, :test do
  gem 'sqlite3', '1.3.13'
  gem 'byebug',  '9.0.6', platform: :mri
end

group :development do
  gem 'web-console',           '3.5.1'
  gem 'listen',                '3.1.5'
  gem 'spring',                '2.0.2'
  gem 'spring-watcher-listen', '2.0.1'
end

group :test do
  gem 'rails-controller-testing', '1.0.2'
  gem 'minitest',                 '5.11.3'
  gem 'minitest-reporters',       '1.1.14'
  gem 'guard',                    '2.13.0'
  gem 'guard-minitest',           '2.4.4'
end

group :production do
  gem 'pg', '0.20.0'
end

# Windows環境ではtzinfo-dataというgemを含める必要があります
gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]

GemLockFile

GEM
  remote: https://rubygems.org/
  specs:
    actioncable (5.1.6)
      actionpack (= 5.1.6)
      nio4r (~> 2.0)
      websocket-driver (~> 0.6.1)
    actionmailer (5.1.6)
      actionpack (= 5.1.6)
      actionview (= 5.1.6)
      activejob (= 5.1.6)
      mail (~> 2.5, >= 2.5.4)
      rails-dom-testing (~> 2.0)
    actionpack (5.1.6)
      actionview (= 5.1.6)
      activesupport (= 5.1.6)
      rack (~> 2.0)
      rack-test (>= 0.6.3)
      rails-dom-testing (~> 2.0)
      rails-html-sanitizer (~> 1.0, >= 1.0.2)
    actionview (5.1.6)
      activesupport (= 5.1.6)
      builder (~> 3.1)
      erubi (~> 1.4)
      rails-dom-testing (~> 2.0)
      rails-html-sanitizer (~> 1.0, >= 1.0.3)
    activejob (5.1.6)
      activesupport (= 5.1.6)
      globalid (>= 0.3.6)
    activemodel (5.1.6)
      activesupport (= 5.1.6)
    activerecord (5.1.6)
      activemodel (= 5.1.6)
      activesupport (= 5.1.6)
      arel (~> 8.0)
    activesupport (5.1.6)
      concurrent-ruby (~> 1.0, >= 1.0.2)
      i18n (>= 0.7, < 2)
      minitest (~> 5.1)
      tzinfo (~> 1.1)
    ansi (1.5.0)
    arel (8.0.0)
    autoprefixer-rails (9.1.4)
      execjs
    bindex (0.5.0)
    bootstrap-sass (3.3.7)
      autoprefixer-rails (>= 5.2.1)
      sass (>= 3.3.4)
    builder (3.2.3)
    byebug (9.0.6)
    coderay (1.1.2)
    coffee-rails (4.2.2)
      coffee-script (>= 2.2.0)
      railties (>= 4.0.0)
    coffee-script (2.4.1)
      coffee-script-source
      execjs
    coffee-script-source (1.12.2)
    concurrent-ruby (1.0.5)
    crass (1.0.4)
    erubi (1.7.1)
    execjs (2.7.0)
    ffi (1.9.25)
    formatador (0.2.5)
    globalid (0.4.1)
      activesupport (>= 4.2.0)
    guard (2.13.0)
      formatador (>= 0.2.4)
      listen (>= 2.7, <= 4.0)
      lumberjack (~> 1.0)
      nenv (~> 0.1)
      notiffany (~> 0.0)
      pry (>= 0.9.12)
      shellany (~> 0.0)
      thor (>= 0.18.1)
    guard-compat (1.2.1)
    guard-minitest (2.4.4)
      guard-compat (~> 1.2)
      minitest (>= 3.0)
    i18n (1.1.0)
      concurrent-ruby (~> 1.0)
    jbuilder (2.7.0)
      activesupport (>= 4.2.0)
      multi_json (>= 1.2)
    jquery-rails (4.3.1)
      rails-dom-testing (>= 1, < 3)
      railties (>= 4.2.0)
      thor (>= 0.14, < 2.0)
    listen (3.1.5)
      rb-fsevent (~> 0.9, >= 0.9.4)
      rb-inotify (~> 0.9, >= 0.9.7)
      ruby_dep (~> 1.2)
    loofah (2.2.2)
      crass (~> 1.0.2)
      nokogiri (>= 1.5.9)
    lumberjack (1.0.13)
    mail (2.7.0)
      mini_mime (>= 0.1.1)
    method_source (0.9.0)
    mini_mime (1.0.1)
    mini_portile2 (2.3.0)
    minitest (5.11.3)
    minitest-reporters (1.1.14)
      ansi
      builder
      minitest (>= 5.0)
      ruby-progressbar
    multi_json (1.13.1)
    nenv (0.3.0)
    nio4r (2.3.1)
    nokogiri (1.8.4)
      mini_portile2 (~> 2.3.0)
    notiffany (0.1.1)
      nenv (~> 0.1)
      shellany (~> 0.0)
    pg (0.20.0)
    pry (0.11.3)
      coderay (~> 1.1.0)
      method_source (~> 0.9.0)
    puma (3.9.1)
    rack (2.0.5)
    rack-test (1.1.0)
      rack (>= 1.0, < 3)
    rails (5.1.6)
      actioncable (= 5.1.6)
      actionmailer (= 5.1.6)
      actionpack (= 5.1.6)
      actionview (= 5.1.6)
      activejob (= 5.1.6)
      activemodel (= 5.1.6)
      activerecord (= 5.1.6)
      activesupport (= 5.1.6)
      bundler (>= 1.3.0)
      railties (= 5.1.6)
      sprockets-rails (>= 2.0.0)
    rails-controller-testing (1.0.2)
      actionpack (~> 5.x, >= 5.0.1)
      actionview (~> 5.x, >= 5.0.1)
      activesupport (~> 5.x)
    rails-dom-testing (2.0.3)
      activesupport (>= 4.2.0)
      nokogiri (>= 1.6)
    rails-html-sanitizer (1.0.4)
      loofah (~> 2.2, >= 2.2.2)
    railties (5.1.6)
      actionpack (= 5.1.6)
      activesupport (= 5.1.6)
      method_source
      rake (>= 0.8.7)
      thor (>= 0.18.1, < 2.0)
    rake (12.3.1)
    rb-fsevent (0.10.3)
    rb-inotify (0.9.10)
      ffi (>= 0.5.0, < 2)
    ruby-progressbar (1.10.0)
    ruby_dep (1.5.0)
    sass (3.6.0)
      sass-listen (~> 4.0.0)
    sass-listen (4.0.0)
      rb-fsevent (~> 0.9, >= 0.9.4)
      rb-inotify (~> 0.9, >= 0.9.7)
    sass-rails (5.0.6)
      railties (>= 4.0.0, < 6)
      sass (~> 3.1)
      sprockets (>= 2.8, < 4.0)
      sprockets-rails (>= 2.0, < 4.0)
      tilt (>= 1.1, < 3)
    shellany (0.0.1)
    spring (2.0.2)
      activesupport (>= 4.2)
    spring-watcher-listen (2.0.1)
      listen (>= 2.7, < 4.0)
      spring (>= 1.2, < 3.0)
    sprockets (3.7.2)
      concurrent-ruby (~> 1.0)
      rack (> 1, < 3)
    sprockets-rails (3.2.1)
      actionpack (>= 4.0)
      activesupport (>= 4.0)
      sprockets (>= 3.0.0)
    sqlite3 (1.3.13)
    thor (0.20.0)
    thread_safe (0.3.6)
    tilt (2.0.8)
    turbolinks (5.0.1)
      turbolinks-source (~> 5)
    turbolinks-source (5.2.0)
    tzinfo (1.2.5)
      thread_safe (~> 0.1)
    uglifier (3.2.0)
      execjs (>= 0.3.0, < 3)
    web-console (3.5.1)
      actionview (>= 5.0)
      activemodel (>= 5.0)
      bindex (>= 0.4.0)
      railties (>= 5.0)
    websocket-driver (0.6.5)
      websocket-extensions (>= 0.1.0)
    websocket-extensions (0.1.3)

PLATFORMS
  ruby

DEPENDENCIES
  bootstrap-sass (= 3.3.7)
  byebug (= 9.0.6)
  coffee-rails (= 4.2.2)
  guard (= 2.13.0)
  guard-minitest (= 2.4.4)
  jbuilder (= 2.7.0)
  jquery-rails (= 4.3.1)
  listen (= 3.1.5)
  minitest (= 5.11.3)
  minitest-reporters (= 1.1.14)
  pg (= 0.20.0)
  puma (= 3.9.1)
  rails (= 5.1.6)
  rails-controller-testing (= 1.0.2)
  sass-rails (= 5.0.6)
  spring (= 2.0.2)
  spring-watcher-listen (= 2.0.1)
  sqlite3 (= 1.3.13)
  turbolinks (= 5.0.1)
  tzinfo-data
  uglifier (= 3.2.0)
  web-console (= 3.5.1)

BUNDLED WITH
   1.16.5