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We had a similar issue a couple months ago.
There might be a conflict between one of your crons and their cron for maintenance scripts.
The cron to run log rotation runs at 00:00
directadmin has some issues with large log files, that if it can't process such large log within 1 minute, it starts all over again the next minute and can cause things to hang
Do you have one of your own crons running at that time? If so, try to delay it with 10 minutes.
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