El Capitan was on my internal SSD which had 50gb's free space. This one was having this problem and a whole lot of others, like system freeze then kernel panic.
So I've installed a new fresh copy of Sierra on a 2TB rotational HDD. This one has 1.9 TB free space.
My media and libraries are stored on a Raid5 Pegasus R4, thunderbolt.
Here's my Etrecheck result.
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EtreCheck version: 3.1.2 (334)
Report generated 2016-11-07 17:12:47
Download EtreCheck from https://etrecheck.com
Runtime 2:39
Performance: Excellent
Click the [Support] links for help with non-Apple products.
Click the [Details] links for more information about that line.
Click the [Remove] links to remove adware.
Problem: Beachballing
Hardware Information: ⓘ
Mac Pro (Late 2013)
[Technical Specifications] - [User Guide] - [Warranty & Service]
Mac Pro - model: MacPro6,1
1 3,7 GHz Quad-Core Intel Xeon E5 (Xeon(R)) CPU: 4-core
16 GB RAM Upgradeable - [Instructions]
DIMM1
4 GB DDR3 ECC 1866 MHz ok
DIMM2
4 GB DDR3 ECC 1866 MHz ok
DIMM3
4 GB DDR3 ECC 1866 MHz ok
DIMM4
4 GB DDR3 ECC 1866 MHz ok
Bluetooth: Good - Handoff/Airdrop2 supported
Wireless: Unknown
Video Information: ⓘ
AMD FirePro D300 - VRAM: 2048 MB
AMD FirePro D300 - VRAM: 2048 MB
DELL UP2715K 2560 x 1440
DELL U2312HM 1920 x 1080 @ 60 Hz
DELL U2212HM 1080 x 1920 @ 60 Hz
System Software: ⓘ
macOS Sierra 10.12.1 (16B2657) - Time since boot: about one hour
Disk Information: ⓘ
APPLE SSD SM0256F disk0 : (251 GB) (Solid State - TRIM: Yes)
[Show SMART report]
EFI (disk0s1) <not mounted> : 210 MB
Macintosh HD (disk0s2) /Volumes/Macintosh HD : 207.00 GB (44.02 GB free)
Recovery HD (disk0s3) <not mounted> [Recovery]: 650 MB
BOOTCAMP (disk0s4) /Volumes/BOOTCAMP : 43.14 GB (2.39 GB free)
Elite Pro Dual TBU3 - RAID 0 disk3 : (8 TB) (Rotational)
EFI (disk3s1) <not mounted> : 210 MB
8TB (disk3s2) /Volumes/8TB : 8.00 TB (242.11 GB free)
USB Information: ⓘ
Apple Inc. BRCM20702 Hub
Apple Inc. Bluetooth USB Host Controller
VIA Labs, Inc. USB3.0 Hub
VIA Labs, Inc. USB3.0 Hub
Vantec D400SU3
Western Digital My Book 1230
VIA Labs, Inc. USB2.0 Hub
Apple, Inc. Keyboard Hub
2.4G 2.4G Wireless Device
iLok iLok
Apple Inc. Apple Keyboard
VIA Labs, Inc. USB2.0 Hub
Razer Razer Naga Hex V2
Yamaha Corporation Steinberg UR28M
Thunderbolt Information: ⓘ
Apple Inc. thunderbolt_bus_2
Apple Inc. thunderbolt_bus_1
Promise Technology, Inc. Pegasus R-Series
Apple Inc. thunderbolt_bus_0
Other World Computing Elite Pro Dual TBU3
Configuration files: ⓘ
System Integrity Protection status: disabled
Gatekeeper: ⓘ
Mac App Store and identified developers
Kernel Extensions: ⓘ
/Library/Extensions
[loaded] com.promise.driver.stex (5.2.10 - SDK 10.9 - 2016-11-05) [Support]
[loaded] com.razer.common.razerhid (17.19 - SDK 10.9 - 2016-11-05) [Support]
[loaded] jp.co.yamaha.driver.YamahaSteinbergUSBAudio (1.9.82 - SDK 10.6 - 2016-11-05) [Support]
System Launch Agents: ⓘ
[not loaded] 7 Apple tasks
[loaded] 182 Apple tasks
[running] 90 Apple tasks
System Launch Daemons: ⓘ
[not loaded] 42 Apple tasks
[loaded] 173 Apple tasks
[running] 95 Apple tasks
Launch Agents: ⓘ
[not loaded] com.adobe.AAM.Updater-1.0.plist (2016-11-06) [Support]
[running] com.adobe.AdobeCreativeCloud.plist (2016-11-06) [Support]
[running] com.bjango.istatmenusagent.plist (2016-11-06) [Support]
[running] com.bjango.istatmenusnotifications.plist (2016-11-06) [Support]
[running] com.bjango.istatmenusstatus.plist (2016-11-06) [Support]
[running] com.razer.rzupdater.plist (2016-11-05) [Support]
[not loaded] com.razerzone.rzdeviceengine.plist (2016-11-05) [Support]
Launch Daemons: ⓘ
[running] com.adobe.adobeupdatedaemon.plist (2016-11-06) [Support]
[running] com.adobe.agsservice.plist (2016-11-07) [Support]
[running] com.bjango.istatmenusdaemon.plist (2016-11-06) [Support]
User Launch Agents: ⓘ
[loaded] com.google.keystone.agent.plist (2016-11-07) [Support]
[running] com.spotify.webhelper.plist (2016-11-07) [Support]
[loaded] com.valvesoftware.steamclean.plist (2016-11-07) [Support]
User Login Items: ⓘ
Steam Application (/Applications/Steam.app)
iTunesHelper Application (/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)
Spotify Application Hidden (/Applications/Spotify.app)
uTorrent Application (/Applications/uTorrent.app)
Internet Plug-ins: ⓘ
AdobeAAMDetect: 3.0.0.0 - SDK 10.9 (2016-11-06) [Support]
QuickTime Plugin: 7.7.3 (2016-10-21)
Safari Extensions: ⓘ
LastPass - LastPass - https://lastpass.com (2016-11-05)
3rd Party Preference Panes: ⓘ
Yamaha Steinberg USB (2015-10-09) [Support]
Time Machine: ⓘ
Time Machine not configured!
Top Processes by CPU: ⓘ
3% WindowServer
3% fontd
2% kernel_task
1% iStat Menus Status
1% mdworker(16)
Top Processes by Memory: ⓘ
3.33 GB Final Cut Pro
2.43 GB com.apple.WebKit.WebContent(7)
1.63 GB kernel_task
410 MB Spotify Helper(2)
279 MB mdworker(16)
Virtual Memory Information: ⓘ
3.00 GB Available RAM
57 MB Free RAM
13.00 GB Used RAM
2.95 GB Cached files
0 B Swap Used
Diagnostics Information: ⓘ
Nov 7, 2016, 03:34:04 PM Self test - passed
Nov 7, 2016, 03:28:57 PM /Library/Logs/DiagnosticReports/Creative Cloud_2016-11-07-152857_[redacted].hang
/Applications/Utilities/Adobe Creative Cloud/*/Creative Cloud.app/Contents/MacOS/Creative Cloud
Nov 7, 2016, 03:28:44 PM /Library/Logs/DiagnosticReports/Activity Monitor_2016-11-07-152844_[redacted].hang
/Applications/Utilities/Activity Monitor.app/Contents/MacOS/Activity Monitor
Nov 7, 2016, 03:28:41 PM /Library/Logs/DiagnosticReports/Final Cut Pro_2016-11-07-152841_[redacted].hang
/Applications/Final Cut Pro.app/Contents/MacOS/Final Cut Pro
Nov 6, 2016, 11:55:16 PM ~/Library/Logs/DiagnosticReports/Adobe CEF Helper_2016-11-06-235516_[redacted].crash
com.adobe.acc.HEXHelper - /Library/Application Support/Adobe/*/Adobe CEF Helper.app/Contents/MacOS/Adobe CEF Helper
Nov 5, 2016, 03:42:33 PM /Library/Logs/DiagnosticReports/Activity Monitor_2016-11-05-154233_[redacted].hang
Nov 5, 2016, 03:40:25 PM /Library/Logs/DiagnosticReports/Final Cut Pro_2016-11-05-154025_[redacted].hang
Nov 5, 2016, 12:17:30 PM /Library/Logs/DiagnosticReports/Kernel_2016-11-05-121730_[redacted].panic [Details]
Nov 5, 2016, 11:40:50 AM /Library/Logs/DiagnosticReports/Kernel_2016-11-05-114050_[redacted].panic [Details]
Nov 5, 2016, 11:15:12 AM /Library/Logs/DiagnosticReports/Kernel_2016-11-05-111512_[redacted].panic [Details]
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