The online tool took several hour of work I would hate to do that every 90 days. Any way I think I figured out changing the 10 to a 90 and got this output seems to have a lot of errors.
gary@linux-omo4:~> sudo le.pl --key account.key --csr mydomain.csr --csr-key mydomain.key --crt mydomain.crt --domains “computerpatch.net,www.computerpatch.net,freeportselfstorage.com,www.freeportselfstorage.com,profennoenterprises.com,www.profennoenterprises.com,brunswickmaineselfstorage.com,www.brunswickmaineselfstorage.com,portlandmaineselfstorage.com,www.portlandmaineselfstorage.com” --path /var/www/html/.well-known/acme-challenge/ --generate-missing --unlink --renew 90 --live
[sudo] password for root:
2016/08/09 16:07:34 [ ZeroSSL Crypt::LE client v0.17 started. ]
2016/08/09 16:07:34 Loading an account key from account.key
2016/08/09 16:07:34 Loading a CSR from mydomain.csr
2016/08/09 16:07:34 Checking certificate for expiration (website connection).
2016/08/09 16:07:34 Checking brunswickmaineselfstorage.com
2016/08/09 16:07:34 Expiration threshold set at 90 days, the certificate expires in 89 days - will be renewing.
2016/08/09 16:07:35 Make sure to check TOS at https://letsencrypt.org/documents/LE-SA-v1.1.1-August-1-2016.pdf
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//3PWh6LyAbVdIuh43tle2Dn2hdnd58GMmw32H8NhNf8k’ for domain 'brunswickmaineselfstorage.com’
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//NBUhCyl-KbdSvUsWwnDA-_TGIMNEDJTvjoExHLQdT10’ for domain 'computerpatch.net’
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//AQcibZiwSR3ckC9Jn0rcQPqz9V50CQnQ8aXChNKVZqc’ for domain 'freeportselfstorage.com’
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//C19_JUx5d1x30NkkaAGAYbyQDE0C8adwzeu3lpEe9xc’ for domain 'portlandmaineselfstorage.com’
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//Nh-UZaCJRJsK_xzupyXb2ek1DB_pa4HPffUN_7dU6so’ for domain 'profennoenterprises.com’
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//YGyqEUStwv76wZowwcYhGX9kj6JlsaCpYiJqcX4eSts’ for domain 'www.brunswickmaineselfstorage.com’
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//dN0N22LdS2X-dBJxAl3NDhaFC5IHzTRyknId79AFOaA’ for domain 'www.computerpatch.net’
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//7DoS-oxTKhf0pHbGY1Ouj536lAkNAixaoYv0jRWiR0U’ for domain 'www.freeportselfstorage.com’
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//hV5ijA–fkmrYPZjxW7UHDp7n_bfDNU-1e49os6lXUE’ for domain 'www.portlandmaineselfstorage.com’
2016/08/09 16:07:37 Successfully saved a challenge file ‘/var/www/html/.well-known/acme-challenge//RPzHbw8v6Ab18clENJANzOss7XutqMOnPcGt1FdYBWU’ for domain 'www.profennoenterprises.com’
2016/08/09 16:07:39 Domain verification results for ‘brunswickmaineselfstorage.com’: error. Invalid response from http://brunswickmaineselfstorage.com/.well-known/acme-challenge/3PWh6LyAbVdIuh43tle2Dn2hdnd58GMmw32H8NhNf8k: "
404 Not Found
Not Found
<p"
2016/08/09 16:07:39 Challenge file '/var/www/html/.well-known/acme-challenge//3PWh6LyAbVdIuh43tle2Dn2hdnd58GMmw32H8NhNf8k' has been deleted.
2016/08/09 16:07:41 Domain verification results for 'computerpatch.net': error. Invalid response from http://computerpatch.net/.well-known/acme-challenge/NBUhCyl-KbdSvUsWwnDA-_TGIMNEDJTvjoExHLQdT10: "
File Not Found
"
2016/08/09 16:07:41 Challenge file '/var/www/html/.well-known/acme-challenge//NBUhCyl-KbdSvUsWwnDA-_TGIMNEDJTvjoExHLQdT10' has been deleted.
2016/08/09 16:07:46 Domain verification results for 'freeportselfstorage.com': error. Invalid response from http://freeportselfstorage.com/.well-known/acme-challenge/AQcibZiwSR3ckC9Jn0rcQPqz9V50CQnQ8aXChNKVZqc: "
404 Not Found
Not Found
<p"
2016/08/09 16:07:46 Challenge file '/var/www/html/.well-known/acme-challenge//AQcibZiwSR3ckC9Jn0rcQPqz9V50CQnQ8aXChNKVZqc' has been deleted.
2016/08/09 16:07:48 Domain verification results for 'portlandmaineselfstorage.com': error. Invalid response from http://portlandmaineselfstorage.com/.well-known/acme-challenge/C19_JUx5d1x30NkkaAGAYbyQDE0C8adwzeu3lpEe9xc: "
404 Not Found
Not Found
<p"
2016/08/09 16:07:48 Challenge file '/var/www/html/.well-known/acme-challenge//C19_JUx5d1x30NkkaAGAYbyQDE0C8adwzeu3lpEe9xc' has been deleted.
2016/08/09 16:07:50 Domain verification results for 'profennoenterprises.com': error. Invalid response from http://profennoenterprises.com/.well-known/acme-challenge/Nh-UZaCJRJsK_xzupyXb2ek1DB_pa4HPffUN_7dU6so: "
404 Not Found
Not Found
<p"
2016/08/09 16:07:50 Challenge file '/var/www/html/.well-known/acme-challenge//Nh-UZaCJRJsK_xzupyXb2ek1DB_pa4HPffUN_7dU6so' has been deleted.
2016/08/09 16:07:53 Domain verification results for 'www.brunswickmaineselfstorage.com': error. Invalid response from http://www.brunswickmaineselfstorage.com/.well-known/acme-challenge/YGyqEUStwv76wZowwcYhGX9kj6JlsaCpYiJqcX4eSts: "
404 Not Found
Not Found
<p"
2016/08/09 16:07:53 Challenge file '/var/www/html/.well-known/acme-challenge//YGyqEUStwv76wZowwcYhGX9kj6JlsaCpYiJqcX4eSts' has been deleted.
2016/08/09 16:07:55 Domain verification results for 'www.computerpatch.net': error. Invalid response from http://www.computerpatch.net/.well-known/acme-challenge/dN0N22LdS2X-dBJxAl3NDhaFC5IHzTRyknId79AFOaA: "
File Not Found
"
2016/08/09 16:07:55 Challenge file '/var/www/html/.well-known/acme-challenge//dN0N22LdS2X-dBJxAl3NDhaFC5IHzTRyknId79AFOaA' has been deleted.
2016/08/09 16:07:57 Domain verification results for 'www.freeportselfstorage.com': error. Invalid response from http://www.freeportselfstorage.com/.well-known/acme-challenge/7DoS-oxTKhf0pHbGY1Ouj536lAkNAixaoYv0jRWiR0U: "
404 Not Found
Not Found
<p"
2016/08/09 16:07:57 Challenge file '/var/www/html/.well-known/acme-challenge//7DoS-oxTKhf0pHbGY1Ouj536lAkNAixaoYv0jRWiR0U' has been deleted.
2016/08/09 16:08:00 Domain verification results for 'www.portlandmaineselfstorage.com': error. Invalid response from http://www.portlandmaineselfstorage.com/.well-known/acme-challenge/hV5ijA--fkmrYPZjxW7UHDp7n_bfDNU-1e49os6lXUE: "
404 Not Found
Not Found
<p"
2016/08/09 16:08:00 Challenge file '/var/www/html/.well-known/acme-challenge//hV5ijA--fkmrYPZjxW7UHDp7n_bfDNU-1e49os6lXUE' has been deleted.
2016/08/09 16:08:02 Domain verification results for 'www.profennoenterprises.com': error. Invalid response from http://www.profennoenterprises.com/.well-known/acme-challenge/RPzHbw8v6Ab18clENJANzOss7XutqMOnPcGt1FdYBWU: "
404 Not Found
Not Found
sorry if I posted wrong i don't see code brackets.