EC2 instances in your Elastic Beanstalk environment generate logs that you can view to troubleshoot issues with your application or configuration files. You can easily retrieve them by using the environment management console or the EB CLI.
Via the console you can pull the last 100 lines of the most commonly used log files. The ones probably of most interest will be eb-activity.log and eb-commandprocessor.log as these logs contain messages about deployment activities and particular stack traces associated with errors during deployment.
Its possible there is a more detailed error message which may help to understand what the issue is.
I have also noticed that after setting up an environment (cloning or from scratch) it says it's "ready" sooner then it really is. I found I have to wait another 10-20 minutes sometimes after the env says "ready" before I can change the Configurations or Deploy to it.
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