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MySQL 5.6 Reference Manual
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B.4.4.6 Deleting Rows from Related Tables

If the total length of the DELETE statement for related_table is more than 1MB (the default value of the max_allowed_packet system variable), you should split it into smaller parts and execute multiple DELETE statements. You probably get the fastest DELETE by specifying only 100 to 1,000 related_column values per statement if the related_column is indexed. If the related_column isn't indexed, the speed is independent of the number of arguments in the IN clause.