I’ve had a report from my users that the count.seqs function in Mothur doesn’t work and just produces an empty table - this is also what I’m seeing when testing it both on the current July 2015 distribution, plus I went back to my backup server still running the May 2015 version.
I’ve attached a test set and using the latest Mothur installation and running count.seqs on this seems to work according to the logs but the output file is empty. Datatype needs to be set to names when this is imported of course. I would like to get this working because at the moment my users have to go back to the CLI version to do their work.