All MySQL databases disappeared on my server - recovered one website but not others

I have 2 websites on my server on 2 different IP addresses. I have managed to bring back the first by adding: open_files_limit = 200000 via SSH. I added the same to the second website but it made no difference. When I go into cpanel MySQLDatabases, there are no websites or users, but when I try to re-add the database name it comes back with an error saying the database already exists. When I go into phpmyadmin, the database names are there, but when I click on any of them I get the following message: Error SQL query: DocumentationEdit Edit SELECT * FROM data_dictionary.CHARACTER_SETS MySQL said: Documentation #1142 - SELECT command denied to user 'mysite'@'localhost' for table 'CHARACTER_SETS' I then followed the suggestions in another thread on here and ran the following commands in SSH (one after the other): /scripts/upcp/ ~~force /scripts/checkperlmodules ~~force /usr/local/cpanel/bin/setupdbmap and this is the result: [20130919.113942] [10456] Sep 19 11:39:42.972 [10457] dbg: channel: adding 73_sandbox_manual_scores.cf [20130919.113942] [10456] Sep 19 11:39:42.973 [10457] dbg: channel: adding local.cf [20130919.113942] [10456] Sep 19 11:39:42.973 [10457] dbg: channel: adding regression_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.973 [10457] dbg: channel: update complete [20130919.113942] [10456] Sep 19 11:39:42.973 [10457] dbg: generic: cleaning up temporary directory/files [20130919.113942] [10456] Sep 19 11:39:42.974 [10457] dbg: generic: unlinking 20_dynrdns.cf [20130919.113942] [10456] Sep 19 11:39:42.974 [10457] dbg: generic: unlinking 20_head_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.974 [10457] dbg: generic: unlinking 20_fake_helo_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.974 [10457] dbg: generic: unlinking 72_active.cf [20130919.113942] [10456] Sep 19 11:39:42.975 [10457] dbg: generic: unlinking 25_textcat.cf [20130919.113942] [10456] Sep 19 11:39:42.975 [10457] dbg: generic: unlinking 60_adsp_override_dkim.cf [20130919.113942] [10456] Sep 19 11:39:42.975 [10457] dbg: generic: unlinking 30_text_it.cf [20130919.113942] [10456] Sep 19 11:39:42.975 [10457] dbg: generic: unlinking 25_spf.cf [20130919.113942] [10456] Sep 19 11:39:42.976 [10457] dbg: generic: unlinking 20_ratware.cf [20130919.113942] [10456] Sep 19 11:39:42.976 [10457] dbg: generic: unlinking sa-update-pubkey.txt [20130919.113942] [10456] Sep 19 11:39:42.976 [10457] dbg: generic: unlinking 20_freemail_domains.cf [20130919.113942] [10456] Sep 19 11:39:42.976 [10457] dbg: generic: unlinking 30_text_de.cf [20130919.113942] [10456] Sep 19 11:39:42.977 [10457] dbg: generic: unlinking 25_accessdb.cf [20130919.113942] [10456] Sep 19 11:39:42.977 [10457] dbg: generic: unlinking 25_asn.cf [20130919.113942] [10456] Sep 19 11:39:42.977 [10457] dbg: generic: unlinking 25_dkim.cf [20130919.113942] [10456] Sep 19 11:39:42.977 [10457] dbg: generic: unlinking 50_scores.cf [20130919.113942] [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking 20_drugs.cf [20130919.113942] [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking 20_advance_fee.cf [20130919.113942] [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking local.cf [20130919.113942] [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking user_prefs.template [20130919.113942] [10456] Sep 19 11:39:42.978 [10457] dbg: generic: unlinking 73_sandbox_manual_scores.cf [20130919.113942] [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 10_hasbase.cf [20130919.113942] [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 25_uribl.cf [20130919.113942] [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 20_net_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 25_hashcash.cf [20130919.113942] [10456] Sep 19 11:39:42.979 [10457] dbg: generic: unlinking 23_bayes.cf [20130919.113942] [10456] Sep 19 11:39:42.980 [10457] dbg: generic: unlinking 20_compensate.cf [20130919.113942] [10456] Sep 19 11:39:42.980 [10457] dbg: generic: unlinking 20_porn.cf [20130919.113942] [10456] Sep 19 11:39:42.980 [10457] dbg: generic: unlinking 20_uri_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.980 [10457] dbg: generic: unlinking 20_mailspike.cf [20130919.113942] [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 20_aux_tlds.cf [20130919.113942] [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 72_scores.cf [20130919.113942] [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 20_freemail.cf [20130919.113942] [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 25_pyzor.cf [20130919.113942] [10456] Sep 19 11:39:42.981 [10457] dbg: generic: unlinking 60_whitelist_subject.cf [20130919.113942] [10456] Sep 19 11:39:42.982 [10457] dbg: generic: unlinking STATISTICS-set0-72_scores.cf.txt [20130919.113942] [10456] Sep 19 11:39:42.982 [10457] dbg: generic: unlinking 25_antivirus.cf [20130919.113942] [10456] Sep 19 11:39:42.982 [10457] dbg: generic: unlinking 30_text_fr.cf [20130919.113942] [10456] Sep 19 11:39:42.982 [10457] dbg: generic: unlinking STATISTICS-set1-72_scores.cf.txt [20130919.113942] [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking 60_whitelist_spf.cf [20130919.113942] [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking 20_vbounce.cf [20130919.113942] [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking STATISTICS-set3-72_scores.cf.txt [20130919.113942] [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking 20_imageinfo.cf [20130919.113942] [10456] Sep 19 11:39:42.983 [10457] dbg: generic: unlinking 20_phrases.cf [20130919.113942] [10456] Sep 19 11:39:42.984 [10457] dbg: generic: unlinking 20_html_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.984 [10457] dbg: generic: unlinking 25_razor2.cf [20130919.113942] [10456] Sep 19 11:39:42.984 [10457] dbg: generic: unlinking 30_text_pt_br.cf [20130919.113942] [10456] Sep 19 11:39:42.984 [10457] dbg: generic: unlinking regression_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.985 [10457] dbg: generic: unlinking 10_default_prefs.cf [20130919.113942] [10456] Sep 19 11:39:42.985 [10457] dbg: generic: unlinking languages [20130919.113942] [10456] Sep 19 11:39:42.985 [10457] dbg: generic: unlinking 60_shortcircuit.cf [20130919.113942] [10456] Sep 19 11:39:42.985 [10457] dbg: generic: unlinking 20_meta_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 20_dnsbl_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 60_awl.cf [20130919.113942] [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 30_text_nl.cf [20130919.113942] [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 60_whitelist_dkim.cf [20130919.113942] [10456] Sep 19 11:39:42.986 [10457] dbg: generic: unlinking 30_text_pl.cf [20130919.113942] [10456] Sep 19 11:39:42.987 [10457] dbg: generic: unlinking STATISTICS-set2-72_scores.cf.txt [20130919.113942] [10456] Sep 19 11:39:42.987 [10457] dbg: generic: unlinking 20_body_tests.cf [20130919.113942] [10456] Sep 19 11:39:42.987 [10457] dbg: generic: unlinking 25_dcc.cf [20130919.113942] [10456] Sep 19 11:39:42.987 [10457] dbg: generic: unlinking 60_whitelist.cf [20130919.113942] [10456] Sep 19 11:39:42.988 [10457] dbg: generic: unlinking 25_replace.cf [20130919.113942] [10456] Sep 19 11:39:42.988 [10457] dbg: diag: updates complete, exiting with code 0 [20130919.113943] [10456] Done [20130919.113945] [10456] Checking update....update ok! [20130919.113945] Processing: Restoring compiler permissions [20130919.113945] - Processing command `/usr/local/cpanel/scripts/compilers restore` [20130919.113945] [10460] Compilers are enabled for unprivileged users. [20130919.113945] Processing: Cleaning SpamAssassin DBM files [20130919.113945] - Processing command `/usr/local/cpanel/scripts/spamassassin_dbm_cleaner` [20130919.113945] [10461] /usr/local/cpanel/scripts/spamassassin_dbm_cleaner: version 1.0 [20130919.113945] [10461] Checking SpamAssassin dbm databases....Done [20130919.113945] [10461] Checked 0 files for user(s), ok, broken [20130919.113945] Processing: Configuring Frontpage [20130919.113945] - Processing command `/usr/local/cpanel/scripts/initfpsuexec` [20130919.113945] [10462] initfpsuexec: using apache 1.x support [20130919.113945] [10462] chattr: No such file or directory while trying to stat _vti_bin/fpexe [20130919.113945] [10462] grep: /usr/local/frontpage/version5.0/apache-fp/_vti_bin/fpexe: No such file or directory [20130919.113945] [10462] x - creating lock directory [20130919.113945] [10462] x - extracting /usr/local/frontpage/version5.0/apache-fp/fpexe.c (text) [20130919.113945] [10462] x - creating lock directory [20130919.113945] [10462] x - extracting /usr/local/frontpage/version5.0/apache-fp/fpexe2.patch (text) [20130919.113945] [10462] patching file fpexe.c [20130919.113945] [10462] C compiler (/usr/bin/gcc) OK (cached Thu Sep 19 03:58:38 2013) [20130919.113945] [10462] Tuned C compiler not available because it is not enabled [20130919.113945] [10462] Using Frontpage with suexec [20130919.113945] [10462] /usr/bin/ld: cannot open output file _vti_bin/fpexe: No such file or directory [20130919.113945] [10462] collect2: ld returned 1 exit status [20130919.113945] [10462] chown: cannot access `_vti_bin': No such file or directory [20130919.113945] [10462] chmod: cannot access `_vti_bin/fpexe': No such file or directory [20130919.113945] [10462] chattr: No such file or directory while trying to stat _vti_bin/fpexe [20130919.113945] Cleaning Squirrelmail attachment directories [20130919.113945] Processing: Running former postinstall scripts [20130919.113945] - Processing command `/usr/local/cpanel/bin/dcpumon --killproc` [20130919.113945] [10557] Added Contact myname@myaddress.com [20130919.113945] - Processing command `/usr/local/cpanel/bin/scanfornewmail` [20130919.113945] [10560] Scanning for new mail senders.....Done [20130919.113945] - Processing command `/usr/local/cpanel/scripts/fixsuexeccgiscripts` [20130919.113945] [10561] Scanning suexec_log...Done [20130919.113945] - Processing command `/usr/local/cpanel/bin/setupdbmap` [20130919.113946] - Processing command `/usr/local/cpanel/bin/fix_userdata_perms` [20130919.113946] - Processing command `/usr/local/cpanel/scripts/detect_env_capabilities` [20130919.113946] [20130919.113946] Maintenance complete. => Log closed Thu Sep 19 11:39:46 2013 ---------------------------------------------------------------------------------------------------- => Log opened from cPanel Update (upcp) - Slave at Thu Sep 19 11:39:46 2013 [20130919.113946] Maintenance completed successfully [20130919.113946] Running Standardized hooks [20130919.113946] [20130919.113946] cPanel update completed [20130919.113946] A log of this update is available at /var/cpanel/updatelogs/update.1379587138.log [20130919.113946] Removing upcp pidfile [20130919.113946] [20130919.113946] Completed all updates => Log closed Thu Sep 19 11:39:46 2013 root@972773 [~]# /scripts/checkperlmodules ~~force scripts/checkperlmodules is deprecated. cPanel no longer uses /usr/bin/perl and provides its perl modules as a set of RPMs. For more information, see http://go.cpanel.net/1136checkperlmodules root@972773 [~]# /usr/local/cpanel/bin/setupdbmap info [setupdbmap] Begin setupdbmap info [setupdbmap] Updating MySQL users info [setupdbmap] Processing MySQL databases and database users ... info [setupdbmap] Finished with MySQL users info [setupdbmap] PostgreSQL is not installed. Could not locate executable psql client. info [setupdbmap] End setupdbmap info [setupdbmap] Storing Database Index info [setupdbmap] Database Index Complete root@972773 [~]#
I reaceched mysql databases - still same issue, and rechecked phpmyadmin - also still same. I then tried to a reinstall of my entire site using akeeba backup, but ran into problems again - when I tried to run kickstart (in the same way as I have hundreds of times before) I now get this error: Not Found The requested URL /kickstart.php was not found on this server. Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request. So I appear to be stumped - I can't repair my databases and I can't re-install my site. Its like my cPanel has become corrupted if this is possible. Can you help me? Kind regards Mandy