Progress tracking tool for managing PhD students
Like @Orion suggested, trello is great for organizing work. It is a kanban board where you express tasks as cards and you pile those cards in different decks; usual decks are TO-DO, DOING and DONE, but this is up to you. You can have different boards, one per student. It is collaborative and allows to grant access to a board to specific users (e.g. each student's board would be accessed by the student and you). you can open a card and write comments on it.

If you prefer not to depend on an external service, you can self-host a trello clone, like wekan.

Update: for Gantt charts within the kanban board approach, I see 2 options:


Pay for the Trello extension called elegantt.
Use the open source kanban board called kanboard. It is less visually appealing, but comes with a Gantt view out of the box. You can either host it yourself or subscribe to the hosted version.