They have almost the same meaning, which is "at least". They can be interchangeable depending on the context.
"せめて" is mainly used when you want to mention a minimum requirement in an emotional/subjective way. It indicates your expectations or desires.
"少なくとも" is also used when you want to talk about something in a logical/objective way, and again, in order to mention the minimum requirements for something. It is often used to state something objectively based on factual informaion.
- [OK]健康でいる為に、毎日せめて6時間は寝てね。
- [OK]健康でいる為に、毎日少なくとも6時間は寝てね。
- [OK]せめて最後に一度だけあなたの笑顔を見せてね。
- [NG]少なくとも最後に一度だけあなたの笑顔を見せてね。
- [NG]この地図によれば、せめてここから駅まで10分はかかる。
- [OK]この地図によれば、少なくともここから駅まで10分はかかる。
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