What is the MySQL version? OS? What is innodb_buffer_pool_size? How much RAM is used by other processes?
Then please ...
(i) post the result of ...
select engine,data,indexes,total
from (
select
ifnull(engine,'TOTALS') as engine,
concat(data,' GB') as data,
concat(indexes,' GB') as indexes,
concat(tot,' GB') as total,
if(engine is null,-1,tot) as ord
from (
select
engine,
round( sum(data_length)/1024/1024/1024, 2 ) as data,
round( sum(index_length)/1024/1024/1024, 2 ) as indexes,
round( sum(data_length+index_length)/1024/1024/1024, 2 ) as tot
from information_schema.tables
where engine is not null and engine not in('information_schema','performance_schema')
group by engine with rollup
) sums
) list
order by list.ord desc;
(ii) post the results of running these queries in the mysql client program ...
show variables;
show global status;
(iii) post the result of this OS cmd ...
free -m
(iv) post the result of Show Create Table for the slow table.