Lets Encrypt Cannot Issue Certificate for Domain

I have successfully installed and configure ISPConfig in my server. I have also configured a website in ISPConfig and it is working well. During the creation I did not enable Let's Encrypt. Later when I tried to enable Let's Encrypt I am getting error while issuing a certificate. I have enabled the debug logs in ISPConfig and it shows that "Verified domain XXX.XX should be reachable for letsencrypt." The website is working and when pinged the server from a system outside my network, it showed the correct IP of the server where the domain is hosted. What could be the issue?

Info:
ISPConfig: 3.2.2
OS: Ubuntu 20.04
Webserver: Apache
Database: MySQL
PHP Version: 7.4
Letsencrypt logs:

Code:

2021-02-25 12:06:05,217:DEBUG:certbot.main:certbot version: 0.40.0
2021-02-25 12:06:05,217:DEBUG:certbot.main:Arguments: ['-n', '--text', '--agree-tos', '--expand', '--authenticator', 'webroot', '--server', 'https://acme-v02.api.letsencrypt.org/directory', '--rsa-key-size', '4096', '--email', '[email protected]', '--webroot-map', '{"onewolf.in":"\\/usr\\/local\\/ispconfig\\/interface\\/acme","www.onewolf.in":"\\/usr\\/local\\/ispconfig\\/interface\\/acme"}']
2021-02-25 12:06:05,217:DEBUG:certbot.main:Discovered plugins: PluginsRegistry(PluginEntryPoint#manual,PluginEntryPoint#null,PluginEntryPoint#standalone,PluginEntryPoint#webroot)
2021-02-25 12:06:05,223:DEBUG:certbot.log:Root logging level set at 20
2021-02-25 12:06:05,223:INFO:certbot.log:Saving debug log to /var/log/letsencrypt/letsencrypt.log
2021-02-25 12:06:05,223:DEBUG:certbot.plugins.selection:Requested authenticator webroot and installer None
2021-02-25 12:06:05,223:DEBUG:certbot.plugins.selection:Single candidate plugin: * webroot
Description: Place files in webroot directory
Interfaces: IAuthenticator, IPlugin
Entry point: webroot = certbot.plugins.webroot:Authenticator
Initialized: <certbot.plugins.webroot.Authenticator object at 0x7f736ad35c10>
Prep: True
2021-02-25 12:06:05,223:DEBUG:certbot.plugins.selection:Selected authenticator <certbot.plugins.webroot.Authenticator object at 0x7f736ad35c10> and installer None
2021-02-25 12:06:05,223:INFO:certbot.plugins.selection:Plugins selected: Authenticator webroot, Installer None
2021-02-25 12:06:05,227:DEBUG:certbot.main:Picked account: <Account(RegistrationResource(body=Registration(key=None, contact=(), agreement=None, status=None, terms_of_service_agreed=None, only_return_existing=None, external_account_binding=None), uri='https://acme-v02.api.letsencrypt.org/acme/acct/113024633', new_authzr_uri=None, terms_of_service=None), 4c7e4d46ef21edb08677a334e35140b9, Meta(creation_dt=datetime.datetime(2021, 2, 17, 7, 0, 59, tzinfo=<UTC>), creation_host='mail.sumansa.com'))>
2021-02-25 12:06:05,227:DEBUG:acme.client:Sending GET request to https://acme-v02.api.letsencrypt.org/directory.
2021-02-25 12:06:05,228:DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): acme-v02.api.letsencrypt.org:443
2021-02-25 12:06:06,418:DEBUG:urllib3.connectionpool:https://acme-v02.api.letsencrypt.org:443 "GET /directory HTTP/1.1" 200 658
2021-02-25 12:06:06,419:DEBUG:acme.client:Received response:
HTTP 200
Server: nginx
Date: Thu, 25 Feb 2021 06:36:06 GMT
Content-Type: application/json
Content-Length: 658
Connection: keep-alive
Cache-Control: public, max-age=0, no-cache
X-Frame-Options: DENY
Strict-Transport-Security: max-age=604800

{
  "L7EaJgDovVU": "https://community.letsencrypt.org/t/adding-random-entries-to-the-directory/33417",
  "keyChange": "https://acme-v02.api.letsencrypt.org/acme/key-change",
  "meta": {
    "caaIdentities": [
      "letsencrypt.org"
    ],
    "termsOfService": "https://letsencrypt.org/documents/LE-SA-v1.2-November-15-2017.pdf",
    "website": "https://letsencrypt.org"
  },
  "newAccount": "https://acme-v02.api.letsencrypt.org/acme/new-acct",
  "newNonce": "https://acme-v02.api.letsencrypt.org/acme/new-nonce",
  "newOrder": "https://acme-v02.api.letsencrypt.org/acme/new-order",
  "revokeCert": "https://acme-v02.api.letsencrypt.org/acme/revoke-cert"
}
2021-02-25 12:06:06,421:DEBUG:certbot.cert_manager:Renewal conf file /etc/letsencrypt/renewal/eden144.com.conf is broken. Skipping.
2021-02-25 12:06:06,422:DEBUG:certbot.cert_manager:Traceback was:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/certbot/cert_manager.py", line 382, in _search_lineages
    candidate_lineage = storage.RenewableCert(renewal_file, cli_config)
  File "/usr/lib/python3/dist-packages/certbot/storage.py", line 444, in __init__
    raise errors.CertStorageError(
certbot.errors.CertStorageError: renewal config file {} is missing a required file reference

2021-02-25 12:06:06,426:INFO:certbot.main:Obtaining a new certificate
2021-02-25 12:06:06,695:DEBUG:certbot.crypto_util:Generating key (4096 bits): /etc/letsencrypt/keys/0011_key-certbot.pem
2021-02-25 12:06:06,700:DEBUG:certbot.crypto_util:Creating CSR: /etc/letsencrypt/csr/0011_csr-certbot.pem
2021-02-25 12:06:06,700:DEBUG:acme.client:Requesting fresh nonce
2021-02-25 12:06:06,700:DEBUG:acme.client:Sending HEAD request to https://acme-v02.api.letsencrypt.org/acme/new-nonce.
2021-02-25 12:06:06,985:DEBUG:urllib3.connectionpool:https://acme-v02.api.letsencrypt.org:443 "HEAD /acme/new-nonce HTTP/1.1" 200 0
2021-02-25 12:06:06,986:DEBUG:acme.client:Received response:
HTTP 200
Server: nginx
Date: Thu, 25 Feb 2021 06:36:06 GMT
Connection: keep-alive
Cache-Control: public, max-age=0, no-cache
Link: <https://acme-v02.api.letsencrypt.org/directory>;rel="index"
Replay-Nonce: 0004WIsQV9YEp0kwINHgK3TAx-6rkNbiJYxfeEOORFnf7PA
X-Frame-Options: DENY
Strict-Transport-Security: max-age=604800


2021-02-25 12:06:06,988:DEBUG:acme.client:Storing nonce: 0004WIsQV9YEp0kwINHgK3TAx-6rkNbiJYxfeEOORFnf7PA
2021-02-25 12:06:06,989:DEBUG:acme.client:JWS payload:
b'{\n  "identifiers": [\n    {\n      "type": "dns",\n      "value": "onewolf.in"\n    },\n    {\n      "type": "dns",\n      "value": "www.onewolf.in"\n    }\n  ]\n}'
2021-02-25 12:06:07,008:DEBUG:acme.client:Sending POST request to https://acme-v02.api.letsencrypt.org/acme/new-order:
{
  "protected": "eyJhbGciOiAiUlMyNTYiLCAia2lkIjogImh0dHBzOi8vYWNtZS12MDIuYXBpLmxldHNlbmNyeXB0Lm9yZy9hY21lL2FjY3QvMTEzMDI0NjMzIiwgIm5vbmNlIjogIjAwMDRXSXNRVjlZRXAwa3dJTkhnSzNUQXgtNnJrTmJpSll4ZmVFT09SRm5mN1BBIiwgInVybCI6ICJodHRwczovL2FjbWUtdjAyLmFwaS5sZXRzZW5jcnlwdC5vcmcvYWNtZS9uZXctb3JkZXIifQ",
  "signature": "GTIztZJxTPvsGP4FUU2PHnY1r4U0y0P5kCNPsNt5FLJS9IU9eX7AgclQ81ayEnSuy5pTLazieCLDjxYqiiTpWnCYZsSYx7jtp53qzVvzQpQ6ESi9giQ7jNWRaYFLhDwtUtB2C8en3Z78UY6TrXI3RoxlUtIIFvqCwj6tY7naR_SJzh9ts4_m3RxDDUdNzZcXrS-3iFmurDZNStk5EwaeBtNEbJWxv6yIRb1Xvr3gUVyxBnn9GxE1fChZS5kcXbCILiJ-1OV-bQud8JlhXnDaf_WRMpDD8rHieY4vVvIJEVZZyj0hqy13SfN8aLglYsPKStoUFHpEW_R2P0A3thkrv8t8Wv2q7nUNHgNPB3Ip5tnM8Uzq-G_qac86ZcmdvhSIJKXGYTkS_e7RzGa-Ivj9Je8Hov0gIyGIm1Qjix7CslIee8bp2cyXUHu_W1RnSlLCWdHUA6TWZUO-_Ed4YY9snPkMVLsJpPyefGL9uNkhvIRlQxSYcYXnA58SfNvg6L4gIe4dZcoa1XD5p3aNGfQCohKdQXh8YrRBl7YL7d9pELt99Y9HP76xoDAAwu9xPq2pX64bZ8eRr_CjaeZthq2R2N4vq3rQhNWjaMDT7RT0qsWf-iwX6XMIN4mhfzatz2eVr5BxYmwKmxHU2ckKnrWmhShGRdy4KoViRt7f4MD8KCw",
  "payload": "ewogICJpZGVudGlmaWVycyI6IFsKICAgIHsKICAgICAgInR5cGUiOiAiZG5zIiwKICAgICAgInZhbHVlIjogIm9uZXdvbGYuaW4iCiAgICB9LAogICAgewogICAgICAidHlwZSI6ICJkbnMiLAogICAgICAidmFsdWUiOiAid3d3Lm9uZXdvbGYuaW4iCiAgICB9CiAgXQp9"
}
2021-02-25 12:06:07,305:DEBUG:urllib3.connectionpool:https://acme-v02.api.letsencrypt.org:443 "POST /acme/new-order HTTP/1.1" 429 250
2021-02-25 12:06:07,306:DEBUG:acme.client:Received response:
HTTP 429
Server: nginx
Date: Thu, 25 Feb 2021 06:36:07 GMT
Content-Type: application/problem+json
Content-Length: 250
Connection: keep-alive
Boulder-Requester: 113024633
Cache-Control: public, max-age=0, no-cache
Link: <https://acme-v02.api.letsencrypt.org/directory>;rel="index"
Replay-Nonce: 0004059vzgTo-CqJfTWM-_NjymKX904kytGXvjk2Zah8Dr8

{
  "type": "urn:ietf:params:acme:error:rateLimited",
  "detail": "Error creating new order :: too many certificates already issued for exact set of domains: onewolf.in,www.onewolf.in: see https://letsencrypt.org/docs/rate-limits/",
  "status": 429
}
2021-02-25 12:06:07,307:DEBUG:certbot.log:Exiting abnormally:
Traceback (most recent call last):
  File "/bin/letsencrypt", line 11, in <module>
    load_entry_point('certbot==0.40.0', 'console_scripts', 'certbot')()
  File "/usr/lib/python3/dist-packages/certbot/main.py", line 1382, in main
    return config.func(config, plugins)
  File "/usr/lib/python3/dist-packages/certbot/main.py", line 1265, in certonly
    lineage = _get_and_save_cert(le_client, config, domains, certname, lineage)
  File "/usr/lib/python3/dist-packages/certbot/main.py", line 121, in _get_and_save_cert
    lineage = le_client.obtain_and_enroll_certificate(domains, certname)
  File "/usr/lib/python3/dist-packages/certbot/client.py", line 417, in obtain_and_enroll_certificate
    cert, chain, key, _ = self.obtain_certificate(domains)
  File "/usr/lib/python3/dist-packages/certbot/client.py", line 348, in obtain_certificate
    orderr = self._get_order_and_authorizations(csr.data, self.config.allow_subset_of_names)
  File "/usr/lib/python3/dist-packages/certbot/client.py", line 381, in _get_order_and_authorizations
    orderr = self.acme.new_order(csr_pem)
  File "/usr/lib/python3/dist-packages/acme/client.py", line 863, in new_order
    return self.client.new_order(csr_pem)
  File "/usr/lib/python3/dist-packages/acme/client.py", line 666, in new_order
    response = self._post(self.directory['newOrder'], order)
  File "/usr/lib/python3/dist-packages/acme/client.py", line 95, in _post
    return self.net.post(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/acme/client.py", line 1171, in post
    return self._post_once(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/acme/client.py", line 1184, in _post_once
    response = self._check_response(response, content_type=content_type)
  File "/usr/lib/python3/dist-packages/acme/client.py", line 1042, in _check_response
    raise messages.Error.from_json(jobj)
acme.messages.Error: urn:ietf:params:acme:error:rateLimited :: There were too many requests of a given type :: Error creating new order :: too many certificates already issued for exact set of domains: onewolf.in,www.onewolf.in: see https://letsencrypt.org/docs/rate-limits/
2021-02-25 12:06:07,310:ERROR:certbot.log:An unexpected error occurred:
2021-02-25 12:06:07,310:ERROR:certbot.log:There were too many requests of a given type :: Error creating new order :: too many certificates already issued for exact set of domains: onewolf.in,www.onewolf.in: see https://letsencrypt.org/docs/rate-limits/
2021-02-25 12:06:07,542:DEBUG:certbot.main:certbot version: 0.40.0
2021-02-25 12:06:07,542:DEBUG:certbot.main:Arguments: ['--domains', 'onewolf.in', '--domains', 'www.onewolf.in']
2021-02-25 12:06:07,542:DEBUG:certbot.main:Discovered plugins: PluginsRegistry(PluginEntryPoint#manual,PluginEntryPoint#null,PluginEntryPoint#standalone,PluginEntryPoint#webroot)
2021-02-25 12:06:07,547:DEBUG:certbot.log:Root logging level set at 20
2021-02-25 12:06:07,547:INFO:certbot.log:Saving debug log to /var/log/letsencrypt/letsencrypt.log
2021-02-25 12:06:07,547:WARNING:certbot.cert_manager:Renewal configuration file /etc/letsencrypt/renewal/eden144.com.conf produced an unexpected error: renewal config file {} is missing a required file reference. Skipping.
2021-02-25 12:06:07,548:DEBUG:certbot.cert_manager:Traceback was:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/certbot/cert_manager.py", line 79, in certificates
    renewal_candidate = storage.RenewableCert(renewal_file, config)
  File "/usr/lib/python3/dist-packages/certbot/storage.py", line 444, in __init__
    raise errors.CertStorageError(
certbot.errors.CertStorageError: renewal config file {} is missing a required file reference

2021-02-25 12:06:07,549:WARNING:certbot.cert_manager:Renewal configuration file /etc/letsencrypt/renewal/mail.sumansa.com.conf produced an unexpected error: fullchain does not match cert + chain for mail.sumansa.com!. Skipping.
2021-02-25 12:06:07,549:DEBUG:certbot.cert_manager:Traceback was:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/certbot/cert_manager.py", line 80, in certificates
    crypto_util.verify_renewable_cert(renewal_candidate)
  File "/usr/lib/python3/dist-packages/certbot/crypto_util.py", line 221, in verify_renewable_cert
    verify_fullchain(renewable_cert)
  File "/usr/lib/python3/dist-packages/certbot/crypto_util.py", line 324, in verify_fullchain
    raise e
  File "/usr/lib/python3/dist-packages/certbot/crypto_util.py", line 318, in verify_fullchain
    raise errors.Error(error_str)
certbot.errors.Error: fullchain does not match cert + chain for mail.sumansa.com!

 

The domain mail.sumansa.com is the main domain where ISPConfig is configured. Onewolf.in is the domain where LetsEncrypt is unable to issue a certificate.
I configured LetsEncrypt for the domain mail.sumansa.com during ISPConfig's installation but even that is also showing error. The installation of ISPConfig completed successfully and all the modules are functioning except 1)LetsEncrypt cannot issue certificates to any of the domain I create, and 2) I cannot access the ISPConfig's login page without ignoring the certificate warning.

 

Ah, my bad, didn't notice that line. Thanks much.
Any idea about "certbot.errors.Error: fullchain does not match cert + chain for mail.sumansa.com!" ?