What to do if predatory journal won't withdraw paper after acceptance? Last year, I’ve started an independent research in hopes to be published one day.
Fast forwarding a year (a couple of weeks ago in fact), I have finished my manuscript in which I was planning to submit it to an open access journal called Journal of Emerging Infectious Disease with OMICS. At the time, I did not know that OMICS was a predatory journal (after seeing Beall's list) and I’m at the final stages before it get published. 

To clarify, my manuscript has been accepted for publishing BUT during that time, I found out that it was a predatory journal and requested that I retract my manuscript from this journal.  I did not sign anything or pay anything to OMICS. What happened was that they sent me the acceptance letter saying my manuscript got accepted for publishing. They gave me 48 hours to request any changes to the final project of the manuscript before publishing. In that 48 hours, I found out that they were a predatory journal and messaged them accordingly. At this point, I did not sign anything entailing that I sent copyrights to them or payed any fees and it's not published yet.

They advised me that they have made the DOI and it is impossible for them to retract. At this point, I did advise them that I will not approve anything going forward and that they appreciate my request to retract from the journal. 

Given the story that was mentioned above, I was wondering if you have any advise on going forward and if possible, see if there is a possibility that my manuscript will not be published in this predatory journal? I was extremely shocked that these type of practices by journals existed and extremely glad I caught this before accepting anything to be published. I greatly appreciate any advise you will give and hope to hear from you soon.
There are three issues here.  Have you signed a publication agreement, have you paid them, and has the paper actually been published yet?


If all three have happened, then you are probably stuck.  Retracting a published paper is a big deal, since it involves
changing the permanent scholarly record, and you can't do this just
because you regret the choice of journal.
If you have signed and paid, but the paper has not been published yet, then legally they have the right to publish it but you may
have a chance.  An ethical publisher would not publish a paper over
the last-minute objections of the authors.  (Of course the publisher
would be legitimately upset with the authors if there wasn't a
compelling reason for the withdrawal, but they wouldn't insist on
publishing anyway.)  Unfortunately, there's no reason to expect that
a predatory publisher will behave ethically, but it can't hurt to
ask.
If you have signed but not paid, then you have some leverage.  Legally they may be able to demand payment, but actually suing you
would be more trouble than it is worth.  They probably don't want to
publish the paper without being paid, so you may be able to negotiate
a withdrawal.  On the other hand, it's conceivable that they would
publish the paper in order to strengthen their legal/ethical case for
getting paid.
If you have not yet signed, then there's nothing they can do, since publishing the paper without your permission would be a
copyright violation.  You should be polite but firm, and they will
have to accept that you have withdrawn the submission.