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Might be a n00b question. I have an IIS server with a site where I can host our website. But if I host the same website as an application in an existing site, it gives us a 500 error.

But my question is how do I go about debugging it? Event logs show no related entries, IIS logs just show the HTTP GET messages but no errors, disabling 'display friendly http errors' does nothing, failed request trace is configured but empty.

How do I find the error?

It's a ASP.NET site

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There is a similar question on SO Detailed 500 error message, ASP + IIS 7.5

Also check that the ASP.Net version (e.g. 1.1, 2.0 or 4) has been set correctly in the Web Site properties.

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