Respect order, see Capistrano vars http://theadmin.org/articles/capistrano-variables/
production.rb
server 'saap', user: 'alfredo', roles: %w{web app db}, primary: true
set :deploy_to, '/home/alfredo/rails_apps/saap/'
set :whenever_command, lambda { "cd #{release_path} && sudo /opt/rubies/ruby-2.2.0/lib/ruby/gems/2.2.0/gems/bundler-1.10.6/bin/bundle exec whenever -i -u alfredo" }
set :whenever_identifier, 'saap'
Full paths for logging files
schedule.rb
set :output, { error: "/home/alfredo/rails_apps/saap/current/log/cron_error.log", standard: "/home/alfredo/rails_apps/saap/current/log/cron.log" }