I assume you are referring to the "Java Runtime Analysis Toolkit"?
I recommend that you run the Latest Stinger,Mcafee Rootkit Remover,followed up by running Malwarebytes (Free) Version only.
All of these Superb (Free) Tools can be found below my Signature (Second Link)
Please pay close attention to (How to use) in regards to Stinger/Rootkit Remover.
You may want to run McAfee Getsusp as well. Kindly list your Email address under "Preferences" before scanning.
If all it was was "JRAT" then McAfee should be able to detect and remove it anyway. However there may be something else attached. What symptoms are you seeing and what operating system and service pack is this?
Have you thought of trying System Restore to go back to before it happened?
If successful then temporarily disable System Restore to delete the infection.
There are some other suggestion in the last link in my signature below.
"JRAT" could be the Java Runtime Analysis Toolkit, but it could also refer to a Java Remote Access Trojan. The post did not make clear how the presence of this, whatever it is, became evident.
Knowing the file name might help, but it would be better to upload the file to VirusTotal for checking by a range of antimalware products. All we know is that it was scanned, presumably by McAfee, and the scan found nothing.
It's not possible to give any advice until we get some more information about the file.