Logstash - shutdown process appears to be stalled

Elastic Stack Logstash
1

I am getting this error out of nowhere. Logstash was running correctly and then this error occured,

[2017-05-08T10:16:43,819][WARN ][logstash.agent           ] stopping pipeline {:id=>"main"}
[2017-05-08T10:16:49,190][WARN ][logstash.shutdownwatcher ] {"inflight_count"=>0, "stalling_thread_info"=>{"other"=>[{"thread_id"=>24, "name"=>"[main]<beats", "current_call"=>"[...]/vendor/bundle/jruby/1.9/gems/logstash-input-beats-3.1.15-java/lib/logstash/inputs/beats.rb:196:in `run'"}, {"thread_id"=>22, "name"=>"[main]>worker0", "current_call"=>"[...]/logstash-core/lib/logstash/util/wrapped_synchronous_queue.rb:127:in `synchronize'"}]}}
[2017-05-08T10:16:49,193][ERROR][logstash.shutdownwatcher ] The shutdown process appears to be stalled due to busy or blocked plugins. Check the logs for more information.

This is my logstash conf file,

input {
    beats {
        port => "5043"
    }
}


filter {
   if [type] in ["grafana", "netdata", "api"] {
         grok{
           match => [ "message" , "%{COMBINEDAPACHELOG}+%{GREEDYDATA:extra_fields}"]
           overwrite => [ "message" ]
         }
        mutate {
           convert => ["response", "integer"]
           convert => ["bytes", "integer"]
           convert => ["responsetime", "float"]
         }
        geoip {
           source => "clientip"
           target => "geoip"
           add_tag => [ "nginx-geoip" ]
        }
        date {
           match => [ "timestamp" , "dd/MMM/YYYY:HH:mm:ss Z" ]
           remove_field => [ "timestamp" ]
        }
        useragent {
           source => "agent"
        }
   }

}

output {
      elasticsearch {
        hosts => [ "localhost:9200" ]
        index => "%{type}_indexer"
    } 
}

Every thing was running good, I just restarted it and this error came up.

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