Writing referee report: found major error, now what? I'm writing a referee report on a paper.  This paper is interesting and, if correct, would be worth publishing. However, I believe they have a major mistake in their method which invalidates their results more or less entirely. I am 90%+ confident that this method is in error, which will affect their results in (possibly unpredictable) ways.

How should I address this in the rest of the paper? I could write the rest of the referee report assuming that they haven't made this mistake - but I think that could be a waste of my time (and their time, since it'll take me longer to do).  

If a referee had this sort of problem with your paper, what would you like to happen?

Edited to add: 
One of the major concerns I have with just rejecting, focusing on this point (as recommended by Raghu and others), is the (time and $) cost of re-running things. Saying, "This is wrong" but not going through the rest of the paper could lead to a second referee report where they've fixed the error and re-done everything.  If I then say, "Also, Experiment B doesn't mean what you think it does," re-running Experiment B may have been a waste. How much consideration of these factors do you think a referee owes the authors?
If there's a "major mistake in their method which invalidates their results more or less entirely" it seems pretty clear that you should explain this in your review, and not bother writing much else. (This seems so obvious, I wonder if I'm misunderstanding your question.) Why on earth would you "write the rest of the referee report assuming that they haven't made this mistake," if you're quite sure that the mistake exists, and that it invalidates most of the paper? What purpose would it serve, for the authors or future readers?