I am also in an almost similar dilemma. I am a final year PhD student. In our university, we are required to published 3 papers in top level journals (SCI) as part of PhD graduation requirements. By late last year, I had submitted 3 papers but had not gotten acceptance on any. So I decided to submit a paper to a conference which was a subset of one of the papers submitted to journals. At the beginning of the year, I was lucky and got acceptance of 2 journal papers, hence I decided to withdraw the conference paper mid January and did not participate. However, end of February, my supervisor accidentally discovered the paper I had submitted to the conference without his knowledge had been published and was online, he is the second author yet he was not aware. He is now mad at me and has threatened to disqualify me from graduating this July. The conference I submitted the paper to turned out to be a fake conference and have refused to withdraw and remove my paper from the publications online despite my numerous appeals to them. Every time I get a chance to meet my supervisor, he would only quarrel me that I must withdraw the paper. What should I do to reconcile with my supervisor and convince him to allow me to graduate.