As I don't know the openssl command's arguments by heart, I am used to referring to the same Stack Overflow answer whenever I need to create self-signed certificates (for testing environments). The command looks like:
openssl req -x509 -nodes -newkey rsa:2048 -keyout mysite.key -out mysite.crt -days 365
And it usually works, for instance on my current Ubuntu 15.10. Today I'm on a fresh install of Debian Jessie and it doesn't. Apache warns at startup that:
[ssl:warn] [pid 1040] AH01906: www.mysite.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)
I looked for a solution to the problem and found an answer in a Linux forum stating that the following should be used instead:
openssl genrsa -des3 -passout pass:x -out mysite.pass.key 2048
openssl rsa -passin pass:x -in mysite.pass.key -out mysite.key
openssl req -new -key mysite.key -out mysite.csr
openssl x509 -req -days 365 -in mysite.csr -signkey mysite.key -out mysite.crt
And it's true, this way the Apache warning disappears.
As far as I understand, this creates a passphrase-protected key, then removes the passphrase, then creates a CSR, then generates the certificate with both the CSR and the key.
So the question is: what does this longer version do that the shorter doesn't, and why is it necessary in some cases (like today for me)?
Short way (e.g. with OpenSSL 1.1.0f and Apache 2.4.37):
openssl genrsa -out notEncodedPk.key 3072
openssl req -new -out website.csr -sha256 -key notEncodedPk.key
openssl x509 -req -in website.csr -days 365 -signkey notEncodedPk.key -out website.cert -outform PEM
genrsa generates a 3072 bit RSA-Key. (The system should be online for some time to have good data in /dev/(u)random for seeding.) There is no need to generate an encrypted PK (1) and then use rsa to remove the password afterwards. (Maybe earlier versions of the tools required a password?)
req creates the certificate signing request and uses the PK for the signature. Providing something like -sha256 for the digest is optional. (3) Provide your infos in the interactive questionare. Ensure to put your site domain in "Common name:", otherwise the Apache will throw a warning (AH01909) and browsers will throw an "invalid certificate" message because the URL/domain does not match the certificate data (2). Leave "A challange password:" empty.
Use x509 to create a self-signed certificate with -signkey (the subject is copied to issuer). Normally the command works on certificates but with -req it accepts a CSR as an input. Then use your PK for signing the certificate. (-outform and -days are optional, with 30 days as the default value for the latter.)
Problem source:
As user207421 already stated: req creates a CSR OR it creates a self-signed root-CA-like certificate, therefore the typical tutorial tip
openssl req -x509 -nodes -days 365 -newkey rsa:3072 -sha256 -keyout website.key -out website.cert
is short but normally not what you want. You can also compare created certificates with
openssl x509 -text -noout -in website.cert
In the certificate, created with the single-line command, you see a section "X509v3 extensions:" with "X509v3 Basic Constraints: critical CA:TRUE". This is exactly the Apache warning message.
Instead, if you create the certificate with the three steps, the "X509v3 extensions:" section is not included into the certificate.
Appendix:
(1) Securing the PK with a password is a good idea in most cases. If the PK is stored without encryption, make sure to restrict access to root. If you use a password, you have to use the -passout/-passin options, but be aware that a simple "x" does not work anymore because some OpenSSL tools require at least 4 characters (otherwise: "result too small/bad password read"). Additionally in Apache you have to use something like SSLPassPhraseDialog buildin to manually enter the required password for the PK (or even for all PKs/certs) during Apache startup.
(2) Anyway, browsers will display a warning for self-signed certificates.
(3) Using SHA-1 would be inadequate for such a large RSA-key. In general, it is a good idea to review your openssl.conf, e.g. in Debian 9 in /etc/ssl/openssl.conf, which contains various defaults, for example signer_digest = sha256.
In the Debian 9 file, you also find in the [req] section a line x509_extensions=v3_ca and this is the reason, why the req command in combination with the -x509 option adds the CA-related extension (basicContraints=critical,CA:true), if used in the single-line style to create a self-signed certificate.
Addidionally you might notice a comment-line # req_extensions=v3_req. Because this line is commented out (in Debian 9 default openssl.cnf), the simple usage of the req command does not include any extensions.
Note that you might use this line in a modified file to add Subject Alternative Name's to the certificate, e.g. so it can handle multiple (sub-)domains (normally a much better choice than using e wildcard in CN, e.g. *.example.com).