Hi ! Thanks in advance for your help…
I’m using read.otu command. Usually, everything flies perfectly with mothur, but not today with the new files I’m processing…

So I have on one hand 701 16S sequences, well aligned with aligned.seqs. My objective is to finish the work by using tree.shared.
The command read.dist works fine. However when I move to read.otu(list=my-file-here-, group=my-names-here,…) the command indicates:

“Error: sequence XXXXXX was not found in the group file”…while in fact if I check…this sequence is present in the group file…

Do you have any idea of what’s happening ?

Thanks for your answer,


I suspect that your group names might have a space in them. The only space that is allowed in the group file is a tab between the sequence and group names.

That’s the problem: I can confirm that there is a tab and not a space between the names of the sequences and the names of groups. Also the error message only appear for one sequence…and if I suppress this sequence, the same error message appear for an other sequence, for which the problem has not been detected before…

Have you seen that before ?
Thanks for sharing your experience


When mothur encounters a sequence that is not in the group file, it bails. The error message is not a list of all sequences not found in the group file, just the first one. If you want to send your files to I can take a look. :slight_smile: