I thought my e file was completed in March and check already sent to IRS. I found my e file was not submitted. What do I do now and will there be a penalty?

[Opus 17]

If you owe tax and both filed and paid late, but are less than 30 days late, the penalty is 5% of the amount you owed.  The IRS will send you a bill.  If this is the first time you have ever owed a penalty, you can request a waiver.  

https://www.irs.gov/businesses/small-businesses-self-employed/penalty-relief

[Opus 17]

Did you file and pay now? That’s the first step.  If you paid by check in March and only filed late, I think the penalty for late filing only is 1% of what you owed or less.