The following command has the same output:
/root/letsencrypt/letsencrypt-auto certonly --manual -d example.org
2016-04-08 21:17:05,410:ERROR:letsencrypt.crypto_util:[('PEM routines', 'PEM_read_bio', 'no start line')] Traceback (most recent call last): File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/crypto_util.py", line 226, in _get_sans_from_cert_or_req cert_or_req = load_func(typ, cert_or_req_str) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/OpenSSL/crypto.py", line 1511, in load_certificate _raise_current_error() File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/OpenSSL/_util.py", line 48, in exception_from_error_queue raise exception_type(errors) Error: [('PEM routines', 'PEM_read_bio', 'no start line')] 2016-04-08 21:17:05,420:DEBUG:letsencrypt.main:Exiting abnormally: Traceback (most recent call last): File "/root/.local/share/letsencrypt/bin/letsencrypt", line 11, in <module> sys.exit(main()) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/main.py", line 692, in main return config.func(config, plugins) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/main.py", line 509, in obtain_cert _, action = _auth_from_domains(le_client, config, domains, lineage) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/main.py", line 76, in _auth_from_domains action, lineage = _treat_as_renewal(config, domains) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/main.py", line 212, in _treat_as_renewal ident_names_cert, subset_names_cert = _find_duplicative_certs(config, domains) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/main.py", line 243, in _find_duplicative_certs candidate_names = set(candidate_lineage.names()) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/storage.py", line 604, in names return crypto_util.get_sans_from_cert(f.read()) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/crypto_util.py", line 245, in get_sans_from_cert cert, OpenSSL.crypto.load_certificate, typ) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/letsencrypt/crypto_util.py", line 226, in _get_sans_from_cert_or_req cert_or_req = load_func(typ, cert_or_req_str) File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/OpenSSL/crypto.py", line 1511, in load_certificate _raise_current_error() File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/OpenSSL/_util.py", line 48, in exception_from_error_queue raise exception_type(errors) Error: [('PEM routines', 'PEM_read_bio', 'no start line')]