The catalina.pid is missing in your case.
This file is located under {your_jira_dir}/work/catalina.pid and it contains the pid of the current instance of jira.
so
ps aux | grep jira
- find the correct entry
- Copy the PID of the output and create a file that only contains this PID. - Make sure it can be read and written by the user which runs jira.
- Try to shutdown jira again.