tente não usar ORDER-BY e LIMIT para um número tão pequeno de atualizações.
UPDATE companies t1
join
(
SELECT c.id,@RowNum:[email protected]+1 AS RowID
FROM companies c, (SELECT @RowNum := 0)r
WHERE c.crawling = 0 AND c.url_host IS NOT NULL
ORDER BY c.last_crawled ASC
)t2
ON t2.RowID=1 AND t1.id=t2.id
SET t1.crawling = 1
EDITAR:1
certifique-se de ter o índice em (last_crawled ASC , id ASC)
UPDATE companies t1
join
(
Select ID,RowID
From
(
SELECT c.id,@RowNum:[email protected]+1 AS RowID
FROM companies c, (SELECT @RowNum := 0)r
WHERE c.crawling = 0 AND c.url_host IS NOT NULL
ORDER BY c.last_crawled ASC
)t2
WHERE ROWID=1
)t3
ON t1.id=t3.id
SET t1.crawling = 1
