I have a similar issue like this and I have upgraded to latest version 5.0 to see if the issue goes away but I still see the same issue.
below is the configuration and few debug lines where it mentions the file is
- paths: - /apps/opt/logs/*/*/*.log exclude_lines: ["^DEBUG"] input_type: log ignore_older: 1m close_inactive: 10s clean_removed: true clean_inactive: 10s close_removed: true close_renamed: true #force_close_files: true scan_frequency: 5s
2016/11/08 23:49:43.090250 prospector_log.go:269: DBG File rename was detected: /apps/opt/logs/application.log -> /apps/opt/logs/application.23_08Nov2016.34.log, Current offset: 21675185
2016/11/08 23:49:43.090275 prospector_log.go:282: DBG File rename detected but harvester not finished yet.
2016/11/08 23:49:43.090304 prospector_log.go:288: DBG Harvester for file is still running: /apps/opt/logs/application.23_08Nov2016.34.log
any help is appreciated.