The Discovery Tree "Hide techs which require locked essential techs" setting is set does not show any techs past Automation Science with Lignumis installed. The pre-requisite and layer settings seem to work correctly but if I enable the Essential techs setting I can't see any possible techs to research.

I can reproduce the issue on a new save with only the Space Age mods, Lignumis, and Discovery Tree enabled by starting a new file and debug unlocking Automation Science.
/c game.player.force.technologies['automation-science-pack '].researched=true

I tried locking automation and the iron/copper plate techs in the editor then unlocking them again but it didn't fix the problem. I suspect it's related to Automation Science not actually having any requirement for cost or triggers.

Thank you.

Just tested in my save and if I research every tech that is a direct dependency of automation science then the essential techs setting in discovery tree start working correctly again.

I don't get this mod. It all makes no sense. I don't think that's something for me to fix. Maybe ask the author of the other mod?

I did a little testing with a local copy of Lignumis and fixed the bug by changing
automation_science_pack_technology.enabled = from false to true
in \lignumis\prototypes\integrations\vanilla.lua

It looks like DiscoveryTree skips over techs that are disabled.
line 39 of control.lua > if t.valid and t.prototype.enabled then

If you need AutomationScience to be disabled I can reach out to the creator of DiscoveryTree.