Here you are:
root@jira:/etc/filebeat# /usr/share/filebeat/bin/filebeat -e -d "*"
2018-09-07T12:23:51.421Z INFO instance/beat.go:544 Home path: [/usr/share/filebeat/bin] Config path: [/usr/share/filebeat/bin] Data path: [/usr/share/filebeat/bin/data] Logs path: [/usr/share/filebeat/bin/logs]
2018-09-07T12:23:51.421Z DEBUG [beat] instance/beat.go:571 Beat metadata path: /usr/share/filebeat/bin/data/meta.json
2018-09-07T12:23:51.449Z INFO instance/beat.go:551 Beat UUID: d3bdd3ba-5b90-468c-80fa-79f3857968bb
2018-09-07T12:23:51.449Z DEBUG [seccomp] seccomp/seccomp.go:109 Loading syscall filter {"seccomp_filter": {"no_new_privs":true,"flag":"tsync","policy":{"default_action":"errno","syscalls":[{"names":["accept","accept4","access","arch_prctl","bind","brk","clock_gettime","clone","close","connect","dup","dup2","epoll_create","epoll_create1","epoll_ctl","epoll_pwait","epoll_wait","exit","exit_group","fchdir","fchmod","fchown","fcntl","fdatasync","flock","fstat","fsync","ftruncate","futex","getcwd","getdents","getdents64","geteuid","getgid","getpeername","getpid","getppid","getrandom","getrusage","getsockname","getsockopt","gettid","gettimeofday","getuid","inotify_add_watch","inotify_init1","inotify_rm_watch","ioctl","kill","listen","lseek","lstat","madvise","mincore","mkdirat","mmap","mprotect","munmap","nanosleep","newfstatat","open","openat","pipe","pipe2","poll","pread64","pselect6","pwrite64","read","readlink","readlinkat","recvfrom","recvmmsg","recvmsg","rename","renameat","rt_sigaction","rt_sigprocmask","rt_sigreturn","sched_getaffinity","sched_yield","sendfile","sendmmsg","sendmsg","sendto","set_robust_list","setitimer","setsockopt","shutdown","sigaltstack","socket","stat","statfs","sysinfo","tgkill","time","tkill","uname","unlink","unlinkat","wait4","waitid","write","writev"],"action":"allow"}]}}}
2018-09-07T12:23:51.450Z INFO [seccomp] seccomp/seccomp.go:116 Syscall filter successfully installed
2018-09-07T12:23:51.451Z INFO [beat] instance/beat.go:768 Beat info {"system_info": {"beat": {"path": {"config": "/usr/share/filebeat/bin", "data": "/usr/share/filebeat/bin/data", "home": "/usr/share/filebeat/bin", "logs": "/usr/share/filebeat/bin/logs"}, "type": "filebeat", "uuid": "d3bdd3ba-5b90-468c-80fa-79f3857968bb"}}}
2018-09-07T12:23:51.451Z INFO [beat] instance/beat.go:777 Build info {"system_info": {"build": {"commit": "34b4e2cc75fbbee5e7149f3916de72fb8892d070", "libbeat": "6.4.0", "time": "2018-08-17T22:20:20.000Z", "version": "6.4.0"}}}
2018-09-07T12:23:51.451Z INFO [beat] instance/beat.go:780 Go runtime info {"system_info": {"go": {"os":"linux","arch":"amd64","max_procs":2,"version":"go1.10.3"}}}
2018-09-07T12:23:51.459Z INFO [beat] instance/beat.go:784 Host info {"system_info": {"host": {"architecture":"x86_64","boot_time":"2018-01-30T08:13:34Z","containerized":false,"hostname":"jira","ips":["127.0.0.1/8","::1/128","10.101.4.4/24","fe80::222:48ff:fe01:1989/64"],"kernel_version":"4.13.0-1007-azure","mac_addresses":["00:22:48:01:19:89"],"os":{"family":"debian","platform":"ubuntu","name":"Ubuntu","version":"16.04.3 LTS (Xenial Xerus)","major":16,"minor":4,"patch":3,"codename":"xenial"},"timezone":"UTC","timezone_offset_sec":0,"id":"3dec2bea2c5747c2b95d853f2a55dbfa"}}}
2018-09-07T12:23:51.460Z INFO [beat] instance/beat.go:813 Process info {"system_info": {"process": {"capabilities": {"inheritable":null,"permitted":["chown","dac_override","dac_read_search","fowner","fsetid","kill","setgid","setuid","setpcap","linux_immutable","net_bind_service","net_broadcast","net_admin","net_raw","ipc_lock","ipc_owner","sys_module","sys_rawio","sys_chroot","sys_ptrace","sys_pacct","sys_admin","sys_boot","sys_nice","sys_resource","sys_time","sys_tty_config","mknod","lease","audit_write","audit_control","setfcap","mac_override","mac_admin","syslog","wake_alarm","block_suspend","audit_read"],"effective":["chown","dac_override","dac_read_search","fowner","fsetid","kill","setgid","setuid","setpcap","linux_immutable","net_bind_service","net_broadcast","net_admin","net_raw","ipc_lock","ipc_owner","sys_module","sys_rawio","sys_chroot","sys_ptrace","sys_pacct","sys_admin","sys_boot","sys_nice","sys_resource","sys_time","sys_tty_config","mknod","lease","audit_write","audit_control","setfcap","mac_override","mac_admin","syslog","wake_alarm","block_suspend","audit_read"],"bounding":["chown","dac_override","dac_read_search","fowner","fsetid","kill","setgid","setuid","setpcap","linux_immutable","net_bind_service","net_broadcast","net_admin","net_raw","ipc_lock","ipc_owner","sys_module","sys_rawio","sys_chroot","sys_ptrace","sys_pacct","sys_admin","sys_boot","sys_nice","sys_resource","sys_time","sys_tty_config","mknod","lease","audit_write","audit_control","setfcap","mac_override","mac_admin","syslog","wake_alarm","block_suspend","audit_read"],"ambient":null}, "cwd": "/etc/filebeat", "exe": "/usr/share/filebeat/bin/filebeat", "name": "filebeat", "pid": 7716, "ppid": 7174, "seccomp": {"mode":"filter","no_new_privs":true}, "start_time": "2018-09-07T12:23:51.300Z"}}}
2018-09-07T12:23:51.461Z INFO instance/beat.go:273 Setup Beat: filebeat; Version: 6.4.0
2018-09-07T12:23:51.461Z DEBUG [beat] instance/beat.go:290 Initializing output plugins
2018-09-07T12:23:51.461Z DEBUG [processors] processors/processor.go:66 Processors:
2018-09-07T12:23:51.462Z DEBUG [publish] pipeline/consumer.go:137 start pipeline event consumer
2018-09-07T12:23:51.462Z INFO pipeline/module.go:98 Beat name: jira
2018-09-07T12:23:51.463Z WARN [cfgwarn] beater/filebeat.go:78 DEPRECATED: prospectors are deprecated, Use `inputs` instead. Will be removed in version: 7.0.0
2018-09-07T12:23:51.469Z ERROR fileset/modules.go:118 Not loading modules. Module directory not found: /usr/share/filebeat/bin/module
2018-09-07T12:23:51.469Z INFO [monitoring] log/log.go:114 Starting metrics logging every 30s
2018-09-07T12:23:51.469Z INFO instance/beat.go:367 filebeat start running.
2018-09-07T12:23:51.469Z INFO registrar/registrar.go:97 No registry file found under: /usr/share/filebeat/bin/data/registry. Creating a new registry file.
2018-09-07T12:23:51.469Z DEBUG [registrar] registrar/registrar.go:400 Write registry file: /usr/share/filebeat/bin/data/registry
2018-09-07T12:23:51.527Z DEBUG [registrar] registrar/registrar.go:393 Registry file updated. 0 states written.
2018-09-07T12:23:51.528Z INFO registrar/registrar.go:134 Loading registrar data from /usr/share/filebeat/bin/data/registry
I have just realized that it is not using /var/lib/filebeat/registry file ...