When i use command ‘classify.seqs’, these sentences show like below.

‘Z32747’ is in your template file and is not in your taxonomy file. Please correct.

It took 8 seconds get probabilities.

The mothur output that all sequence names(eg. Z32747) are not in the taxonomy file.

I checked many times that same names with template file is in the taxonomy file.

I run mothur under the 64bit window version.

Please let me know the solution^^

Try running the set.dir(debug=t) command before you run the classify.seqs command. It will spit out what mothur is reading. The most common problem we see is spaces in the taxonomies.