My system has a problem with El captain
I up dated my system from Yosemite to El Capitian and the mail system stopped at the database update element and the system is not working.
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It sounds like your drive is having problems Vs the upgrading of the OS here.
First I would clean off as much junk as you can try to free up at least 1/4 of the disk. Then run a utility to clean out the old cache & log files like this one: Disk Doctor.
Once you have clean things out you'll need to run Disk Utility from an external drive. If you have a disk already prepped with a bootable OS restart your system so its the active boot disk and then run Disk Utilities First Aid function to repair the disk.
See if that fixes things. If not you may need to go a bit deeper here running a more advanced drive repair program as well as defrag your disk. I would recommend Drive Genius for fixing a hard drive, SSD's don't not need defrag'ing.
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It would be helpful knowing the model you have as Apple has produced quite a few variations. Go to the About This Mac and paste what you have here for us to see.
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