I took my 98 honda civic automatic to O'reilly auto parts they said my code said catalyst system low?

The wording that comes up on the Honda scanner is Catalytic converter is beyond threshold. In short you need a new catalytic converter...depending on what model civic you have depends on how much your going to pay. If you have a civic EX then the catalytic converter is a stand alone converter and is underneath the car. If the car is not an EX then the catalytic converter is part of the exhaust manifold...ouch this one is the expense one...the most common problem is that the manifold cracks right where the the O2 sensor and is leaking exhaust under the Hood...the problem with this is that when the manifold cracks like that it makes it very difficult to remove the O2 sensors. Yes I sad sensors there are 2 sensors in the manifold and if they cannot be removed due to age and possibly rust then you must replace them with FACTORY PARTS NOT PARTS YOU GET FROM O'REILEYS OR AUTO ZONE. The reason for this is that most aftermarket parts are made to fit a wide range of cars. Well you need one that is made for that car and you can only get that from Honda. If you use an after market O2 sensor it will give all kinds of false codes like fuel metering to lean or rich or another catalytic converter code and will cause drive ability problems. If you have a civic EX you have some options but here is what I would keep in mind. If you decide to get an aftermarket converter make sure it is a direct bolt-on replacement. The biggest problem we find is that if the aftermarket converter doesn't fix the problem the you have to use a factory replacement but when you get an aftermarket converter the usually cut off all the attachment points where the factory replacement will go...so that means replacement of almost the complete exhaust system. And let me tell you that is not cheap...the catalytic converter will run you around $650 plus O2 sensor that run about $250 each plus gaskets oh and by the way scrap metal places will pay about $80 for your old converter so don't leave it behind at the shop...that's free money ...I hope this was helpful ...good luck