How badly does a failed course affect me getting into a good Ph. D programme?

I'm currently doing a master's degree by research and my grades for the coursework are as follows: B+, F, A, A, A, A, A. I've submitted two papers to scientific journals and I'm worried that the F will prevent me for getting entry into a good Ph. D programme. Since, it's a degree by research it doesn't have any coursework component and thus no GPA.