Logstash 6.2.4 crashing due to no timestamp error

I have a pipeline that has been running for some time, it had a config that has been defined but we just started using. sending nginx logs using example nginx config from 6.x logstash docs example.

[2018-05-30T20:59:52,223][FATAL][logstash.runner ] An unexpected error occurred! {:error=> # <LogStash::Error: timestamp field is missing>, :backtrace=>["org/logstash/ext/JrubyEventExtLibrary.java:168:insprintf'", "/usr/share/logstash/vendor/bundle/jruby/2.3.0/gems/logstash-output-elasticsearch-9.1.1-java/lib/logstash/outputs/elasticsearch/common.rb:46:in event_action_tuple'", "/usr/share/logstash/vendor/bundle/jruby/2.3.0/gems/logstash-output-elasticsearch-9.1.1-java/lib/logstash/outputs/elasticsearch/common.rb:36:inblock in multi_receive'", "org/jruby/RubyArray.java:2486:in map'", "/usr/share/logstash/vendor/bundle/jruby/2.3.0/gems/logstash-output-elasticsearch-9.1.1-java/lib/logstash/outputs/elasticsearch/common.rb:36:inmulti_receive'", "/usr/share/logstash/logstash-core/lib/logstash/output_delegator_strategies/shared.rb:13:in multi_receive'", "/usr/share/logstash/logstash-core/lib/logstash/output_delegator.rb:49:inmulti_receive'", "/usr/share/logstash/logstash-core/lib/logstash/pipeline.rb:477:in block in output_batch'", "org/jruby/RubyHash.java:1343:ineach'", "/usr/share/logstash/logstash-core/lib/logstash/pipeline.rb:476:in output_batch'", "/usr/share/logstash/logstash-core/lib/logstash/pipeline.rb:428:inworker_loop'", "/usr/share/logstash/logstash-core/lib/logstash/pipeline.rb:386:in block in start_workers'"]}

logstash 6.2.4




config 
    input {
  beats {
    port => 5044
  }
}
filter {
      if [fields][log_type] == "auth" {
      grok {
        match => { "message" => ["%{SYSLOGTIMESTAMP:[system][auth][timestamp]} %{SYSLOGHOST:[system][auth][hostname]} sshd(?:\[%{POSINT:[system][auth][pid]}\])?: %{DATA:[system][auth][ssh][event]} %{DATA:[system][auth][ssh][method]} for (invalid user )?%{DATA:[system][auth][user]} from %{IPORHOST:[system][auth][ssh][ip]} port %{NUMBER:[system][auth][ssh][port]} ssh2(: %{GREEDYDATA:[system][auth][ssh][signature]})?",
                  "%{SYSLOGTIMESTAMP:[system][auth][timestamp]} %{SYSLOGHOST:[system][auth][hostname]} sshd(?:\[%{POSINT:[system][auth][pid]}\])?: %{DATA:[system][auth][ssh][event]} user %{DATA:[system][auth][user]} from %{IPORHOST:[system][auth][ssh][ip]}",
                  "%{SYSLOGTIMESTAMP:[system][auth][timestamp]} %{SYSLOGHOST:[system][auth][hostname]} sshd(?:\[%{POSINT:[system][auth][pid]}\])?: Did not receive identification string from %{IPORHOST:[system][auth][ssh][dropped_ip]}",
                  "%{SYSLOGTIMESTAMP:[system][auth][timestamp]} %{SYSLOGHOST:[system][auth][hostname]} sudo(?:\[%{POSINT:[system][auth][pid]}\])?: \s*%{DATA:[system][auth][user]} :( %{DATA:[system][auth][sudo][error]} ;)? TTY=%{DATA:[system][auth][sudo][tty]} ; PWD=%{DATA:[system][auth][sudo][pwd]} ; USER=%{DATA:[system][auth][sudo][user]} ; COMMAND=%{GREEDYDATA:[system][auth][sudo][command]}",
                  "%{SYSLOGTIMESTAMP:[system][auth][timestamp]} %{SYSLOGHOST:[system][auth][hostname]} groupadd(?:\[%{POSINT:[system][auth][pid]}\])?: new group: name=%{DATA:system.auth.groupadd.name}, GID=%{NUMBER:system.auth.groupadd.gid}",
                  "%{SYSLOGTIMESTAMP:[system][auth][timestamp]} %{SYSLOGHOST:[system][auth][hostname]} useradd(?:\[%{POSINT:[system][auth][pid]}\])?: new user: name=%{DATA:[system][auth][user][add][name]}, UID=%{NUMBER:[system][auth][user][add][uid]}, GID=%{NUMBER:[system][auth][user][add][gid]}, home=%{DATA:[system][auth][user][add][home]}, shell=%{DATA:[system][auth][user][add][shell]}$",
                  "%{SYSLOGTIMESTAMP:[system][auth][timestamp]} %{SYSLOGHOST:[system][auth][hostname]} %{DATA:[system][auth][program]}(?:\[%{POSINT:[system][auth][pid]}\])?: %{GREEDYMULTILINE:[system][auth][message]}"] }
        pattern_definitions => {
          "GREEDYMULTILINE"=> "(.|\n)*"
        }
        remove_field => "message"
      }
      date {
        match => [ "[system][auth][timestamp]", "MMM  d HH:mm:ss", "MMM dd HH:mm:ss" ]
      }
      geoip {
        source => "[system][auth][ssh][ip]"
        target => "[system][auth][ssh][geoip]"
      }
    }
    else if [fields][log_type] == "syslog" {
      grok {
        match => { "message" => ["%{SYSLOGTIMESTAMP:[system][syslog][timestamp]} %{SYSLOGHOST:[system][syslog][hostname]} %{DATA:[system][syslog][program]}(?:\[%{POSINT:[system][syslog][pid]}\])?: %{GREEDYMULTILINE:[system][syslog][message]}"] }
        pattern_definitions => { "GREEDYMULTILINE" => "(.|\n)*" }
        remove_field => "message"
      }
      date {
        match => [ "[system][syslog][timestamp]", "MMM  d HH:mm:ss", "MMM dd HH:mm:ss" ]
      }
    }
    else if [fileset][module] == "nginx" {
      if [fileset][name] == "access" {
        grok {
          match => { "message" => ["%{IPORHOST:[nginx][access][remote_ip]} - %{DATA:[nginx][access][user_name]} \[%{HTTPDATE:[nginx][access][time]}\] \"%{WORD:[nginx][access][method]} %{DATA:[nginx][access][url]} HTTP/%{NUMBER:[nginx][access][http_version]}\" %{NUMBER:[nginx][access][response_code]} %{NUMBER:[nginx][access][body_sent][bytes]} \"%{DATA:[nginx][access][referrer]}\" \"%{DATA:[nginx][access][agent]}\""] }
          remove_field => "message"
        }
        mutate {
          add_field => { "read_timestamp" => "%{@timestamp}" }
        }
        date {
          match => [ "[nginx][access][time]", "dd/MMM/YYYY:H:m:s Z" ]
          remove_field => "[nginx][access][time]"
        }
        useragent {
          source => "[nginx][access][agent]"
          target => "[nginx][access][user_agent]"
          remove_field => "[nginx][access][agent]"
        }
        geoip {
          source => "[nginx][access][remote_ip]"
          target => "[nginx][access][geoip]"
        }
      }
      else if [fileset][name] == "error" {
        grok {
          match => { "message" => ["%{DATA:[nginx][error][time]} \[%{DATA:[nginx][error][level]}\] %{NUMBER:[nginx][error][pid]}#%{NUMBER:[nginx][error][tid]}: (\*%{NUMBER:[nginx][error][connection_id]} )?%{GREEDYDATA:[nginx][error][message]}"] }
          remove_field => "message"
        }
        mutate {
          rename => { "@timestamp" => "read_timestamp" }
        }
        date {
          match => [ "[nginx][error][time]", "YYYY/MM/dd H:m:s" ]
          remove_field => "[nginx][error][time]"
        }
      }
    }

  }


output {
  stdout { codec => rubydebug }
  elasticsearch {
   hosts => ["xxxxx:9200"]
    index => "%{[@metadata][beat]}-%{[@metadata][version]}-%{+YYYY.MM.dd}"
  }
}

It seems you've removed the @timestamp field (I thought that was impossible) yet you use %{+YYYY.MM.dd} in the elasticsearch output.

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