Check the instructions in the PDF for your federal tax filing, to make sure you selected to have your federal payment deducted from your bank account. You can e-file a return without authorizing that the payment be deducted from your bank account (by selecting the "pay by check" option). And, you can make a different selection for on the federal return than you did on the state.
If you find you made the selection to have the federal payment deducted from your bank account, you should wait for the IRS to process the payment to avoid a duplicate payment.
If you find you need to pay your federal taxes for a return you have already filed, you can remit your payment electronically to the IRS using the IRS payment website at this link.
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