Did you receive a notice from the IRS saying you did not pay? If not, you may need to wait just a bit for it to process.
You can use the following link to determine the status of your payments and account with the IRS directly. This is your best option at this point in time.
View your IRS account
If the IRS ever says you did not make your payment, they will send you a notice. You should retain a copy of the cancelled check and a copy of the bank statement with your tax return. You will then be able to reply to any notices sent to you with these copies to prove that you made the payment. The notices will give you information on how to reply to the IRS as well as a number to call if you have issues.
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