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I did have this happen to me, but it turned out there was a flaw in the stopper. When I used a different stopper, it worked just fine with no leaks. (I just happened to have an extra because my cats got one of my test tubes and played with it until it broke...)
 

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I know you arn't supposed to do so but I usually use my finger. PH, kh, gh, nitrate, phosphate. I'm still alive. Sometimes I kind of swirl the tube around without capping it, but usually I cap it with a finger or thumb.
 
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