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Have I understood correctly that when CSR is signed with openssl x509 tool, a CA database index file is not updating ? As opposite, when signing with openssl ca tool, then index file is updating.

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This is correct. openssl x509 is only a tool to manipulate and create certificates, but it is not a standalone CA and does not keep any status. Whereas openssl ca is described in the documentation as:

The ca command is a minimal CA application. It can be used to sign certificate requests in a variety of forms and generate CRLs it also maintains a text database of issued certificates and their status.

This text database includes the index file you refer too.

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