Not a major bug… looks like it is caused by MEGAN.vmoptions not being loaded as part of a ‘tools-only installation’ (option 2).
How to recreate on centos7
#Select to install tools (option 2)
grep: /home/aaron.dickey/megan/tools/…/MEGAN.vmoptions: No such file or directory
Thank you for the bug report. This is indeed broken (in multiple ways) and so I will remove the option to install only selected parts.