Hey there, you are missing chest 3 and chest 5.
When you reach the second conflux, before the final boss, chest 3 is straight ahead, and chest 5 is to the left. You may have ignored them due to going left and forward at the first conflux. However despite the rooms being the same, those went to different areas.
(first conflux = exotic perk upgrades, second conflux = catalysts).
Despite the quest's wording, the 'first chest' is not the first chest in the activity, it is chest 3. Similarly, chest 5 is the 'second chest' and chest 7 (which you've got, right portal on the second conflux) is the 'third chest' for the purpose of the catalyst quests.
Thank you, so do I have to complete the catalyst quest first then I can unlock the upgrades like subsistence destabilizing rounds etc. from the chest that I’ve been opening?
It is the chests that you are missing, that will complete the catalyst quests. When you open chest 3, that will complete the first quest, and you should open chest 5 during the same session. When you go to hand the first catalyst quest in, you'll then auto complete the second and third.
The only catalyst chest you've opened so far is 7, which is for the third catalyst. None of the others relate to the catalysts.