Did you have Filebeat working properly at one point? Did you experience any kind of power failure or hard shutdown?
You should be able to remove the registry file at /var/lib/filebeat/registry and Filebeat should start.
It sounds like you might be experiencing this issue: https://github.com/elastic/beats/issues/3537 Can you please leave a comment on the Github issue saying you are also affected by it if you think it's the same issue.