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It won't matter whether you use lifecycle rules or COPY - the cost will be the same (although in the case of using the CLI, it might be more because you also have to pay for the LIST calls that the CLI initiates because of the --recursive flag).
When you do a COPY from S3 Standard to Glacier Instant Retrieval, you will still pay $0.02 per 1,000 requests according to the S3 pricing page. You will NOT be paying $0.005 per 1,000 requests (that's if you do a COPY into S3 Standard). There's no way to avoid paying for that $4,000 if you put it into Glacier Instant Retrieval because it costs AWS money to put it in that storage system on the backend.
The only other option is to consolidate those files using something like EMR s3-dist-cp, so instead of having 200 million you could potentially only have a few million objects. Then you can use lifecycle rules to easily transition those objects, and that would be much cheaper in terms of the transition fees.
Not a direct answer to your question, which is about the cost of COPY operations, but this Community Article pretty much describes exactly what it is you want to do https://repost.aws/articles/ARO4VRts2vRva3XVsbWrUyGw/optimizing-storage-costs-by-transitioning-millions-of-s3-objects-from-standard-to-glacier-tier
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Agree with this answer, the COPY command is going to be doing a PUT into glacier, so the glacier price is the one to use.
Thanks a ton, I didn't realize that I will be paying for the destination storage class's COPY price, not the source's, and in this case it matches exactly the price of the lifecycle transition cost.