есть директории с _0 в конце? system/query_log и рядом с ней system/query_log_0. и так для каждой таблицы.
https://kb.altinity.com/altinity-kb-setup-and-maintenance/altinity-kb-system-tables-eat-my-disk/ Note 2: Log tables with numeric postfixes (_1 / 2 / 3 …) query_log_1 query_thread_log_3 are results of Clickhouse upgrades. When a new version of Clickhouse starts and discovers that a system log table’s schema is incompatible with a new schema, then Clickhouse renames the old query_log table to the name with the prefix and creates a table with the new schema. You can drop such tables if you don’t need such historic data.
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