Atlas is stuck

As I was running the corrupted nexus for the Atlas quest, I died immediately after killing the boss and completing the map and I had no revive. I can't run it again since it is completely, so I asked in chat and they told me maybe I could try with another nexus, I did and it did not advance the quest.
I think I missed some trigger and now my atlas quests are stuck.
(I have not played Atlas in PoE1 so I am not sure of what should have happened)