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So, solved?

yes thanks, marked

im running it locally, my mac is handeling it OK , through a GUI  terminal, 

i got server shutdown on my VPS, don't know why,

anyways, im doing currently 1 million at a time and i removed a section from the former query

UPDATE worldcitylist 
INNER JOIN worldregionlist as country ON (worldcitylist.countrycode=country.countrycode)
SET worldcitylist.country_id = country.country_id
WHERE id BETWEEN 1000000 AND 2000000

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