Logstash 5.4 , i installed freshly in my ubuntu 16.04 server , after starting the logstash there is no logstash file in init.d directory

root@dev01:/etc/systemd/system# sudo /etc/init.d/logstash start
sudo: /etc/init.d/logstash: command not found

i followed this doc
logstash5.4

Since Ubuntu 16.04 uses systemd instead of init, you should try:

sudo systemctl start logstash.service

which is described in the same doc.

root@dev01:/usr/share/logstash# sudo bin/logstash --path.settings /etc/logstash -f /etc/logstash/conf.d/02-beats-input.conf --config.test_and_exit
ERROR: Failed to parse YAML file "/etc/logstash/logstash.yml". Please confirm if the YAML structure is valid (e.g. look for incorrect usage of whitespace or indentation). Aborting... parser_error=>(): expected , but found BlockMappingStart while parsing a block mapping at line 138 column 2

This implies there is something wrong in your configuration file on line 138. You should check there first.