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I am trying to run my flask app where it makes api calls, runs a ML script on them and prints the results. The issue is this takes a long time and in 5 minutes I always get a 504 error. Is there any way for me to increase the timeout time? If not how would I get around this?

Looks like timeout. What errors do you see in your logs? (link to logs are available on the "Web" page on PythonAnywhere). Also, take a look at https://help.pythonanywhere.com/pages/AsyncInWebApps/