Thanks @schoen, you were right, I have commented script in /etc/cron.d/certbot file
Here is a full log of a fresh try of a renew, if it can helps.
2017-05-30 20:46:22,966:DEBUG:certbot.main:certbot version: 0.14.2
2017-05-30 20:46:22,966:DEBUG:certbot.main:Arguments: ['--standalone', '--renew-by-default', '-d', 'bausse.fr', '-d', 'www.bausse.fr', '-d', 'mail.bausse.fr', '-d', 'smtp.bausse.fr', '-d', 'imap.bausse.fr', '-d', 'mysql.bausse.fr']
2017-05-30 20:46:22,966:DEBUG:certbot.main:Discovered plugins: PluginsRegistry(PluginEntryPoint#apache,PluginEntryPoint#manual,PluginEntryPoint#nginx,PluginEntryPoint#null,PluginEntryPoint#standalone,PluginEntryPoint#webroot)
2017-05-30 20:46:22,995:DEBUG:certbot.plugins.selection:Requested authenticator standalone and installer <certbot.cli._Default object at 0x7ff5c25f9a90>
2017-05-30 20:46:22,995:DEBUG:certbot.cli:Default Detector is Namespace(account=<certbot.cli._Default object at 0x7ff5c2612750>, agree_dev_preview=None, allow_subset_of_names=<certbot.cli._Default object at 0x7ff5c2612510>, apache=<certbot.cli._Default object at 0x7ff5c25f9150>, apache_challenge_location=<certbot.cli._Default object at 0x7ff5c2618d10>, apache_ctl=<certbot.cli._Default object at 0x7ff5c261d150>, apache_dismod=<certbot.cli._Default object at 0x7ff5c2618750>, apache_enmod=<certbot.cli._Default object at 0x7ff5c2618650>, apache_handle_modules=<certbot.cli._Default object at 0x7ff5c2618e90>, apache_handle_sites=<certbot.cli._Default object at 0x7ff5c261d050>, apache_init_script=<certbot.cli._Default object at 0x7ff5c261d250>, apache_le_vhost_ext=<certbot.cli._Default object at 0x7ff5c2618890>, apache_logs_root=<certbot.cli._Default object at 0x7ff5c2618bd0>, apache_server_root=<certbot.cli._Default object at 0x7ff5c26189d0>, apache_vhost_root=<certbot.cli._Default object at 0x7ff5c2618ad0>, authenticator='standalone', break_my_certs=<certbot.cli._Default object at 0x7ff5c2614390>, cert_path=<certbot.cli._Default object at 0x7ff5c2612ad0>, certname=<certbot.cli._Default object at 0x7ff5c25f9910>, chain_path=<certbot.cli._Default object at 0x7ff5c2612490>, checkpoints=<certbot.cli._Default object at 0x7ff5c2614510>, config_dir=<certbot.cli._Default object at 0x7ff5c2612290>, config_file=None, configurator=<certbot.cli._Default object at 0x7ff5c25f9a90>, csr=<certbot.cli._Default object at 0x7ff5c2614a50>, debug=<certbot.cli._Default object at 0x7ff5c2612e50>, debug_challenges=<certbot.cli._Default object at 0x7ff5c2612f50>, dialog=None, domains='mysql.bausse.fr', dry_run=<certbot.cli._Default object at 0x7ff5c25f9a10>, duplicate=<certbot.cli._Default object at 0x7ff5c2612850>, eff_email=<certbot.cli._Default object at 0x7ff5c25f9e10>, email=<certbot.cli._Default object at 0x7ff5c25f9d10>, expand=<certbot.cli._Default object at 0x7ff5c2612150>, force_interactive=<certbot.cli._Default object at 0x7ff5c25f9710>, fullchain_path=<certbot.cli._Default object at 0x7ff5c26126d0>, func=<function certonly at 0x7ff5c284f938>, hsts=<certbot.cli._Default object at 0x7ff5c2614890>, http01_port=<certbot.cli._Default object at 0x7ff5c2614290>, ifaces=<certbot.cli._Default object at 0x7ff5c2612ed0>, init=<certbot.cli._Default object at 0x7ff5c2614310>, installer=<certbot.cli._Default object at 0x7ff5c25f9a90>, key_path=<certbot.cli._Default object at 0x7ff5c26128d0>, logs_dir=<certbot.cli._Default object at 0x7ff5c25f9e90>, manual=<certbot.cli._Default object at 0x7ff5c2618250>, manual_auth_hook=<certbot.cli._Default object at 0x7ff5c2618610>, manual_cleanup_hook=<certbot.cli._Default object at 0x7ff5c261d490>, manual_public_ip_logging_ok=<certbot.cli._Default object at 0x7ff5c261d590>, must_staple=<certbot.cli._Default object at 0x7ff5c2614590>, nginx=<certbot.cli._Default object at 0x7ff5c2661d10>, nginx_ctl=<certbot.cli._Default object at 0x7ff5c261d7d0>, nginx_server_root=<certbot.cli._Default object at 0x7ff5c261d350>, no_bootstrap=<certbot.cli._Default object at 0x7ff5c2612b50>, no_self_upgrade=<certbot.cli._Default object at 0x7ff5c2612a50>, no_verify_ssl=<certbot.cli._Default object at 0x7ff5c2614090>, noninteractive_mode=<certbot.cli._Default object at 0x7ff5c25f92d0>, num=<certbot.cli._Default object at 0x7ff5c2614d10>, os_packages_only=<certbot.cli._Default object at 0x7ff5c2612950>, post_hook=<certbot.cli._Default object at 0x7ff5c26181d0>, pre_hook=<certbot.cli._Default object at 0x7ff5c26180d0>, pref_challs=<certbot.cli._Default object at 0x7ff5c2614f90>, prepare=<certbot.cli._Default object at 0x7ff5c2614110>, quiet=<certbot.cli._Default object at 0x7ff5c2612c50>, reason=<certbot.cli._Default object at 0x7ff5c2614710>, redirect=<certbot.cli._Default object at 0x7ff5c2614690>, register_unsafely_without_email=<certbot.cli._Default object at 0x7ff5c25f9b10>, reinstall=<certbot.cli._Default object at 0x7ff5c2612050>, renew_by_default=True, renew_hook=<certbot.cli._Default object at 0x7ff5c26182d0>, renew_with_new_domains=<certbot.cli._Default object at 0x7ff5c2612410>, rsa_key_size=<certbot.cli._Default object at 0x7ff5c2614490>, server=<certbot.cli._Default object at 0x7ff5c25f9c90>, staging=<certbot.cli._Default object at 0x7ff5c2612d50>, standalone=True, standalone_supported_challenges=<certbot.cli._Default object at 0x7ff5c261d8d0>, staple=<certbot.cli._Default object at 0x7ff5c2614c90>, strict_permissions=<certbot.cli._Default object at 0x7ff5c2614e90>, text_mode=<certbot.cli._Default object at 0x7ff5c25f91d0>, tls_sni_01_port=<certbot.cli._Default object at 0x7ff5c2614190>, tos=<certbot.cli._Default object at 0x7ff5c2612650>, uir=<certbot.cli._Default object at 0x7ff5c2614a90>, update_registration=<certbot.cli._Default object at 0x7ff5c25f9c10>, user_agent=<certbot.cli._Default object at 0x7ff5c2614b10>, validate_hooks=<certbot.cli._Default object at 0x7ff5c26183d0>, verb='certonly', verbose_count=<certbot.cli._Default object at 0x7ff5c2661e90>, webroot=<certbot.cli._Default object at 0x7ff5c2618050>, webroot_map=<certbot.cli._Default object at 0x7ff5c261dad0>, webroot_path=<certbot.cli._Default object at 0x7ff5c261d6d0>, work_dir=<certbot.cli._Default object at 0x7ff5c26120d0>)
2017-05-30 20:46:23,002:DEBUG:certbot.log:Root logging level set at 20
2017-05-30 20:46:23,002:INFO:certbot.log:Saving debug log to /var/log/letsencrypt/letsencrypt.log
2017-05-30 20:46:23,003:DEBUG:certbot.plugins.selection:Requested authenticator standalone and installer None
2017-05-30 20:46:23,065:DEBUG:certbot.plugins.selection:Single candidate plugin: * standalone
Description: Spin up a temporary webserver
Interfaces: IAuthenticator, IPlugin
Entry point: standalone = certbot.plugins.standalone:Authenticator
Initialized: <certbot.plugins.standalone.Authenticator object at 0x7ff5c265f310>
Prep: True
2017-05-30 20:46:23,066:DEBUG:certbot.plugins.selection:Selected authenticator <certbot.plugins.standalone.Authenticator object at 0x7ff5c265f310> and installer None
2017-05-30 20:46:23,068:DEBUG:certbot.main:Picked account: <Account(RegistrationResource(body=Registration(status=None, contact=(u'mailto:jerome@bausse.fr',), agreement=u'https://letsencrypt.org/documents/LE-SA-v1.0.1-July-27-2015.pdf', key=JWKRSA(key=<ComparableRSAKey(<cryptography.hazmat.backends.openssl.rsa._RSAPublicKey object at 0x7ff5c4f3b7d0>)>)), uri=u'https://acme-v01.api.letsencrypt.org/acme/reg/724420', new_authzr_uri=u'https://acme-v01.api.letsencrypt.org/acme/new-authz', terms_of_service=u'https://letsencrypt.org/documents/LE-SA-v1.0.1-July-27-2015.pdf'), 9b903cc2c1731e562ac43b493a5e353f, Meta(creation_host=u'ns3002977.ip-151-80-42.eu', creation_dt=datetime.datetime(2016, 3, 5, 21, 8, 16, tzinfo=)))>
2017-05-30 20:46:23,069:DEBUG:acme.client:Sending GET request to https://acme-v01.api.letsencrypt.org/directory.
2017-05-30 20:46:23,071:DEBUG:requests.packages.urllib3.connectionpool:Starting new HTTPS connection (1): acme-v01.api.letsencrypt.org
2017-05-30 20:46:23,461:DEBUG:requests.packages.urllib3.connectionpool:https://acme-v01.api.letsencrypt.org:443 "GET /directory HTTP/1.1" 200 352
2017-05-30 20:46:23,462:DEBUG:acme.client:Received response:
HTTP 200
Server: nginx
Content-Type: application/json
Content-Length: 352
Boulder-Request-Id: amDRNz_UvRNAqipeHu-0iQBdBI5lFZzcG0hfnPc_K4I
Replay-Nonce: 9u_VEtL3G3SrWoic2QCSVXf0UKWJvWIAAZJM5SGkqkI
X-Frame-Options: DENY
Strict-Transport-Security: max-age=604800
Expires: Tue, 30 May 2017 20:46:28 GMT
Cache-Control: max-age=0, no-cache, no-store
Pragma: no-cache
Date: Tue, 30 May 2017 20:46:28 GMT
Connection: keep-alive
{
"key-change": "https://acme-v01.api.letsencrypt.org/acme/key-change",
"new-authz": "https://acme-v01.api.letsencrypt.org/acme/new-authz",
"new-cert": "https://acme-v01.api.letsencrypt.org/acme/new-cert",
"new-reg": "https://acme-v01.api.letsencrypt.org/acme/new-reg",
"revoke-cert": "https://acme-v01.api.letsencrypt.org/acme/revoke-cert"
}
2017-05-30 20:46:23,470:DEBUG:certbot.renewal:Auto-renewal forced with --force-renewal...
2017-05-30 20:46:23,471:INFO:certbot.main:Renewing an existing certificate
2017-05-30 20:46:23,471:DEBUG:acme.client:Requesting fresh nonce
2017-05-30 20:46:23,471:DEBUG:acme.client:Sending HEAD request to https://acme-v01.api.letsencrypt.org/acme/new-authz.
2017-05-30 20:46:23,656:DEBUG:requests.packages.urllib3.connectionpool:https://acme-v01.api.letsencrypt.org:443 "HEAD /acme/new-authz HTTP/1.1" 405 0
2017-05-30 20:46:23,657:DEBUG:acme.client:Received response:
HTTP 405
Server: nginx
Content-Type: application/problem+json
Content-Length: 91
Allow: POST
Boulder-Request-Id: 7tO9OtwTUlotnghR1j3vyHMrEIb-mJ1NUC755iJ9czk
Replay-Nonce: V8rKmY3NSYJMg7qBlR26adV9TvRRxJAIN3tm8_D5OBA
Expires: Tue, 30 May 2017 20:46:28 GMT
Cache-Control: max-age=0, no-cache, no-store
Pragma: no-cache
Date: Tue, 30 May 2017 20:46:28 GMT
Connection: keep-alive
2017-05-30 20:46:23,657:DEBUG:acme.client:Storing nonce: V8rKmY3NSYJMg7qBlR26adV9TvRRxJAIN3tm8_D5OBA
2017-05-30 20:46:23,658:DEBUG:acme.client:JWS payload:
{
"identifier": {
"type": "dns",
"value": "bausse.fr"
},
"resource": "new-authz"
}
2017-05-30 20:46:23,663:DEBUG:acme.client:Sending POST request to https://acme-v01.api.letsencrypt.org/acme/new-authz:
{
"header": {
"alg": "RS256",
"jwk": {
"e": "AQAB",
"kty": "RSA",
"n": "qVyImOsTcj8mvlld6AJyzw1lZyXYcD3VpObND218ee7dwoJ3Grwk-FeSDI-yx-JzGlcutNyUxDzbA4hiiU-cuF2FVCqo1o9PC4hDymcJwVPrHr2UKtFO_VtzkoUP0itYn3G85hBwtx_pEC_QP10JCr5N3l_0Puu8aCf3AZuAxG0WwuLx9nWCKU-hrlTgxHEuMcWB4B1R2sPP7IP_9uNbfQTeHyvUvSo4RuTN-GCbjxUs8_OJXPvhsc5cgYyYDDOPMnEy6AnGrsC-g1WKYkfPXhkx-xe8rsTn-LcRymGClXlmn35Mg21XalaESADDNT_fkonwM5guXOXtC4ydL1NwMw"
}
},
"protected": "eyJub25jZSI6ICJWOHJLbVkzTlNZSk1nN3FCbFIyNmFkVjlUdlJSeEpBSU4zdG04X0Q1T0JBIn0",
"payload": "ewogICJpZGVudGlmaWVyIjogewogICAgInR5cGUiOiAiZG5zIiwgCiAgICAidmFsdWUiOiAiYmF1c3NlLmZyIgogIH0sIAogICJyZXNvdXJjZSI6ICJuZXctYXV0aHoiCn0",
"signature": "GzigtDq6Xic1SiqUveCbHM0pPO4fq4fs1cVyV_jQRiwHHnS2S_g3ByQv7DGFkzdCrDJEF5mFD9W2FVYMXqw-HpwAmSddSEMolWzvg13iLtrYndebRp95LWcFT3nA0Y54kb9icR9DX80E1g7fAVf6nzQL8kwMmVoqQwbYjTN9YzqwPg25NbM1-9NOSux1dgoQ6tHHF0nzZNlOwZ0Iagem39zjOYU8pmvMEhtS8AcL-b8Vf2ce1SRIOIEp_wGZFqGrG82RMge2fgO91fPsXqjX5wldx6TsfKETSLPnnmok2haktDLOJ0877MkKn7K7He_mHnongP3ySn_J9TIO1dEqtA"
}
2017-05-30 20:46:23,992:DEBUG:requests.packages.urllib3.connectionpool:https://acme-v01.api.letsencrypt.org:443 "POST /acme/new-authz HTTP/1.1" 429 144
2017-05-30 20:46:23,993:DEBUG:acme.client:Received response:
HTTP 429
Server: nginx
Content-Type: application/problem+json
Content-Length: 144
Boulder-Request-Id: m0xQ_WhtWaf54PwqJhFbD15tcjJujpFa18t-Wbn7HRM
Boulder-Requester: 724420
Replay-Nonce: ZSmuqUIjaAUP8bCGeMXkk-qOs6w5ASpXj9uyl-36Zlw
Expires: Tue, 30 May 2017 20:46:28 GMT
Cache-Control: max-age=0, no-cache, no-store
Pragma: no-cache
Date: Tue, 30 May 2017 20:46:28 GMT
Connection: close
{
"type": "urn:acme:error:rateLimited",
"detail": "Error creating new authz :: too many currently pending authorizations",
"status": 429
}
2017-05-30 20:46:23,993:DEBUG:acme.client:Storing nonce: ZSmuqUIjaAUP8bCGeMXkk-qOs6w5ASpXj9uyl-36Zlw
2017-05-30 20:46:23,993:DEBUG:certbot.log:Exiting abnormally:
Traceback (most recent call last):
File "/root/.local/share/letsencrypt/bin/letsencrypt", line 11, in
sys.exit(main())
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/main.py", line 742, in main
return config.func(config, plugins)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/main.py", line 682, in certonly
lineage = _get_and_save_cert(le_client, config, domains, certname, lineage)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/main.py", line 77, in _get_and_save_cert
renewal.renew_cert(config, domains, le_client, lineage)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/renewal.py", line 296, in renew_cert
new_certr, new_chain, new_key, _ = le_client.obtain_certificate(domains)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/client.py", line 313, in obtain_certificate
self.config.allow_subset_of_names)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/auth_handler.py", line 66, in get_authorizations
self.authzr[domain] = self.acme.request_domain_challenges(domain)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/acme/client.py", line 212, in request_domain_challenges
typ=messages.IDENTIFIER_FQDN, value=domain), new_authzr_uri)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/acme/client.py", line 191, in request_challenges
response = self.net.post(self.directory.new_authz, new_authz)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/acme/client.py", line 674, in post
return self._post_once(*args, **kwargs)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/acme/client.py", line 687, in _post_once
return self._check_response(response, content_type=content_type)
File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/acme/client.py", line 574, in _check_response
raise messages.Error.from_json(jobj)
Error: urn:acme:error:rateLimited :: There were too many requests of a given type :: Error creating new authz :: too many currently pending authorizations