Did you noticed these errors:
FATAL: The ssl_crtd helpers are crashing too rapidly, need help!

Squid Cache (Version 3.5.23): Terminated abnormally.
CPU Usage: 63.837 seconds = 28.308 user + 35.529 sys
Maximum Resident Size: 171488 KB
Page faults with physical i/o: 154
2016/12/18 17:25:05| Set Current Directory to /opt/squid-3.5/var/logs/
2016/12/18 17:25:06| Starting Squid Cache version 3.5.23 for 
i386-unknown-freebsd9.3...
2016/12/18 17:25:06| Service Name: squid
2016/12/18 17:25:06| Process ID 2943
2016/12/18 17:25:06| Process Roles: master worker
2016/12/18 17:25:06| NOTICE: Could not increase the number of filedescriptors
2016/12/18 17:25:06| With 32768 file descriptors available
2016/12/18 17:25:06| Initializing IP Cache...
2016/12/18 17:25:06| DNS Socket created at [::], FD 10
2016/12/18 17:25:06| DNS Socket created at 0.0.0.0, FD 11
2016/12/18 17:25:06| Adding domain crownkenya.com from /etc/resolv.conf
2016/12/18 17:25:06| Adding nameserver 192.168.55.254 from /etc/resolv.conf
2016/12/18 17:25:06| helperOpenServers: Starting 5/15 'ssl_crtd' processes
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:06| helperOpenServers: Starting 5/10 'perl' processes
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:06| WARNING: no_suid: setuid(0): (1) Operation not permitted
2016/12/18 17:25:11| Logfile: opening log 
stdio:/opt/squid-3.5/var/logs/access.log

????
And it's good to know you are running FreeBSD 9.3...(32 bit..)

You need to fix the issues with the helpers before anything else since these 
are blockers for squid to operate right.
The missing file is a side effect which happens at almost the same time.
I would have started with looking at the lines:
sslcrtd_program /opt/squid-3.5/libexec/ssl_crtd -s /opt/squid-3.5/ssl_db -M 4MB
store_id_program /usr/local/bin/perl /opt/squid-3.5/scripts/store-id.pl

And see what is causing this operation is not permitted.
It can be rights or another issue but you must resolve it.
And before diving hard into StoreID make sure your squid just runs fine with 
ssl bump.
Then jump into StoreID and feel free to share your wishes for this 
service..(caching youtube, Microsoft updates etc..)

Let me know if you need anything.

Eliezer

----
http://ngtech.co.il/lmgtfy/
Linux System Administrator
Mobile: +972-5-28704261
Email: elie...@ngtech.co.il


From: Odhiambo Washington [mailto:odhia...@gmail.com] 
Sent: Monday, December 19, 2016 1:37 PM
To: Eliezer Croitoru <elie...@ngtech.co.il>
Cc: squid-users@lists.squid-cache.org
Subject: Re: [squid-users] Missing cache files

Hi,

I have added details.txt and also fixed perms on cache.log

On 19 December 2016 at 14:10, Eliezer Croitoru <mailto:elie...@ngtech.co.il> 
wrote:
The file:
http://gw.crownkenya.com/~wash/3.5.22/cache.log.txt

isn't accessible.
Also missing details like OS version and other things.
It seems like a very simple setup and the first thing to check is permissions 
to the whole directory tree:
/opt/squid-3.5/var/cache

Please add the output of:
# ls -la /opt/squid-3.5/var/cache/

Eliezer

----
http://ngtech.co.il/lmgtfy/
Linux System Administrator
Mobile: +972-5-28704261
Email: mailto:elie...@ngtech.co.il


From: squid-users [mailto:mailto:squid-users-boun...@lists.squid-cache.org] On 
Behalf Of Odhiambo Washington
Sent: Monday, December 19, 2016 10:11 AM
To: mailto:squid-users@lists.squid-cache.org
Subject: Re: [squid-users] Missing cache files

Hi Eliezer,

I have put the files on this link: http://bit.ly/2h1bzqp


On 19 December 2016 at 01:38, Eliezer Croitoru 
<mailto:mailto:elie...@ngtech.co.il> wrote:
Can you give more details on the setup?.. squid.conf.
And cache.log dumps.
Files are not usually disappearing but it’s not clear who erased them.
If you do not have a swap file at /opt/squid-3.5/var/cache/ then you should
ask yourself how squid has started at all.

Please fill up the missing pieces,
Eliezer

----
Eliezer Croitoru <http://ngtech.co.il/lmgtfy/>
Linux System Administrator
Mobile: +972-5-28704261
Email: mailto:mailto:elie...@ngtech.co.il


From: squid-users 
[mailto:mailto:mailto:mailto:squid-users-boun...@lists.squid-cache.org] On
Behalf Of Odhiambo Washington
Sent: Saturday, December 17, 2016 12:41 PM
To: mailto:mailto:squid-users@lists.squid-cache.org
Subject: [squid-users] Missing cache files

Hi,

I keep seeing something that I think is odd. Squid has been exiting on
signal 6, and I keep seeing this:

root@gw:/usr/local/openssl # tail -f /opt/squid-3.5/var/logs/cache.log
2016/12/17 13:38:32| DiskThreadsDiskFile::openDone: (2) No such file or
directory
2016/12/17 13:38:32|    /opt/squid-3.5/var/cache/00/26/0000264D
2016/12/17 13:40:24| DiskThreadsDiskFile::openDone: (2) No such file or
directory
2016/12/17 13:40:24|    /opt/squid-3.5/var/cache/00/3B/00003B56
2016/12/17 13:42:34| DiskThreadsDiskFile::openDone: (2) No such file or
directory
2016/12/17 13:42:34|    /opt/squid-3.5/var/cache/00/6B/00006B0D
2016/12/17 13:43:36| DiskThreadsDiskFile::openDone: (2) No such file or
directory
2016/12/17 13:43:36|    /opt/squid-3.5/var/cache/00/00/00000050
2016/12/17 13:44:25| DiskThreadsDiskFile::openDone: (2) No such file or
directory
2016/12/17 13:44:25|    /opt/squid-3.5/var/cache/00/AF/0000AFF1

So, what could be making the files disappear?


--
Best regards,
Odhiambo WASHINGTON,
Nairobi,KE
+254 7 3200 0004/+254 7 2274 3223
"Oh, the cruft."




--
Best regards,
Odhiambo WASHINGTON,
Nairobi,KE
+254 7 3200 0004/+254 7 2274 3223
"Oh, the cruft."




-- 
Best regards,
Odhiambo WASHINGTON,
Nairobi,KE
+254 7 3200 0004/+254 7 2274 3223
"Oh, the cruft."

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