I ran into this issue last night as well.  It seems to me (from looking at 
the beats doco) that beats doesn't handle multiple outputs.  I'm not sure 
how graylog is deciding which output to use but it seems that we can't use 
this type of setup for beats (regardless of the fact that the interface 
allows you to configure it).

Unless I'm missing something completely Beats doesn't seem to have the 
concept of "routes" like nxlog does, there is no way to associate an input 
to an output.

On Tuesday, 6 September 2016 17:57:41 UTC+10, IronCocker wrote:
>
> [root@mirror ~]# more /etc/graylog/collector-sidecar/generated/filebeat.yml
> filebeat:
>   prospectors:
>   - document_type: linux
>     fields:
>       gl2_source_collector: 0d2e5631-e187-4f09-b1a1-562908f44631
>     ignore_older: 0
>     input_type: log
>     paths:
>     - /var/log/*
>     scan_frequency: 10s
>     tail_files: true
>   - document_type: nginx
>     fields:
>       gl2_source_collector: 0d2e5631-e187-4f09-b1a1-562908f44631
>     ignore_older: 0
>     input_type: log
>     paths:
>     - /var/log/nginx/*
>     scan_frequency: 10s
>     tail_files: true
> output:
>   logstash:
>     hosts:
>     - 192.168.1.1:5044
>
> Hi,
>     I configured two tags: *linux* and *nginx*, tag *linux* output ['
> 192.168.1.1:*5044*'], tag *nginx* output ['192.168.1.1:*5055*'], but 
> *filebeat.yml* only have *linux* output, How should i do?
> thx.
>

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