Please contact the IRS for further assistance, 800-829-1040.
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Did you efile? Was your return Accepted? When you efile you get back 2 emails. The first email only confirms the transmission. The second email says if the IRS (or state) Accepted or Rejected your efile. Just paying the fee doesn't file the return. After you paid did you continue on to the very end and hit the big orange Transmit Returns Now button?
Maybe you didn't finish filing it or it Rejected. When you log into your account you should also see the status and if it was Accepted or Rejected, Started, Printed, Ready to Mail, etc. what does it say?