mothur

"screen.seqs" command

It is so strange, all sequence will be move after executing the command of “screen,seqs”.
I would be very appreciate if you could give me some suggests.

You are asking mothur to remove all sequences that do not start at 1 and end at 21000, and none of your samples reach 21000 - they stop at 20518. So mothur removes all of them. What are you trying to do?

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Hello! screen.seqs will remove any read that starts after your specified start value, and any read that ends before your specified end value.

From your summary.seqs output it looks like you should try:
start=1388, end=20318

Good luck with your analysis!

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