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I'm running a DROP COLUMN on the primary key column (I know, it's terrible but I had to do it). There's a progress indicator:

Stage: 1 of 2 'copy to tmp table'    107% of stage done

I haven't been modifying the data during the operation. Why would it be over 100% finished? Will it ever stop?

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Innodb (and in turn xtradb) do not keep running counts of the number of rows in a table. The number of rows displayed when doing a SHOW TABLE STATUS is purely an estimate.

Likely your tool wth the progress indicator is using this information to determine what 100% is. Since it's an estimate, so is the percentage complete.

This article on stackoverflow goes into further detail.

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