Your MySQL is writing temp tables to disk

Your MySQL is writing temp tables to disk
Slow queries on a small box are often silent on-disk temp tables. Check, then raise the ceiling.
— SHOW GLOBAL STATUS LIKE 'Created_tmp_disk_tables';
— if it's climbing, set tmp_table_size = 64M and max_heap_table_size = 64M (keep them equal)
Now GROUP BY and ORDER BY stay in RAM instead of grinding your SSD. Don't go nuts on a 1GB box, 64M per connection adds up. Measure first, then bump. Try it tonight.