I am not seeing any evidence of a duplicate database. It would appear that you have some event scheduled to update your definitions database around 3:14am. Probably no impact on your on-going scan at that time because there were no further updates at that time, but not certain. Normal practice would be to schedule a database update before a scheduled scan.

Lots of variables involved in determining how long a clamscan will require, especially when you say there are active Command Line users, but 8 hours does sound excessive. How long has this been going on?

Look into updating ClamAV to 0.101.2. You are coming up on a year behind and there have been multiple security related patches since 0.100.1 <https://blog.clamav.net/2019/03/clamav-01012-and-01003-patches-have.html>.

-Al-
macOS ClamXAV User

On Mon, May 20, 2019 at 05:08 PM, Clark Dunson via clamav-users wrote:
Hello; 

Running for 525 minutes at >90% CPU seems not good.  Causes noticeable delay in command line activity for all users.

We've got this cronjob:

30 1 * * * /usr/bin/freshclam 2>&1 && /usr/bin/clamscan -o -i -r --quiet / | mail -s "Clam AV Scan Results for $(hostname -s)" itdept@domain.com

on this Linux:

# uname -a
Linux server.domain.com 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Clamscan appeared as the busiest process in top, 8 hours after launch:

PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND                                                                                        
23043 root      20   0  765m 639m 2520 R 90.6 16.2 525:56.48 clamscan                                                                                        
 3071 mysql     20   0 2228m  50m 3552 S  2.3  1.3   4778:31 mysqld                                                                                          
28772 apache    20   0  349m  17m 5652 S  1.7  0.4   0:16.38 httpd

Producing these logs:
--------------------------------------
ClamAV update process started at Sun May 19 01:30:01 2019
WARNING: Your ClamAV installation is OUTDATED!
WARNING: Local version: 0.100.1 Recommended version: 0.101.2
DON'T PANIC! Read https://www.clamav.net/documents/upgrading-clamav
main.cvd is up to date (version: 58, sigs: 4566249, f-level: 60, builder: sigmgr)
Downloading daily-25454.cdiff [100%]
daily.cld updated (version: 25454, sigs: 1574664, f-level: 63, builder: raynman)
bytecode.cld is up to date (version: 328, sigs: 94, f-level: 63, builder: neo)
[LibClamAV] Detected duplicate databases /var/lib/clamav/main.cvd and /var/lib/clamav/main.cld, please manually remove one of them
Database updated (6141007 signatures) from db.local.clamav.net (IP: 104.16.219.84)
--------------------------------------
ClamAV update process started at Sun May 19 03:14:01 2019
WARNING: Your ClamAV installation is OUTDATED!
WARNING: Local version: 0.100.1 Recommended version: 0.101.2
DON'T PANIC! Read https://www.clamav.net/documents/upgrading-clamav
main.cvd is up to date (version: 58, sigs: 4566249, f-level: 60, builder: sigmgr)
daily.cld is up to date (version: 25454, sigs: 1574664, f-level: 63, builder: raynman)
bytecode.cld is up to date (version: 328, sigs: 94, f-level: 63, builder: neo)

Any help would be greatly appreciated!

Thank you -

Clarkman