mgcluster version issues

I am trying to use mgcluster with my 454 metagenomic datasets and have two issues relating to different versions of mothur:

  1. With mothur 1.18.1 (Mac 64 bit), I get the following error when running mgcluster:
    mothur > mgcluster(blast=AMD.blast)

Reading names… 99419 names read.
Reading blast: ||ABError: Sequence ‘003459_AMD_XYG.b2.gene1’ was not found in the names file, please correct

If I provide a names file, I can get around this problem, but this seems like a bug because a names file shouldn’t be necessary, right? When I use mothur 1.15.0 on the same machine, this error is not raised.

  1. If I provide a names file, mglcuster runs successfully on mothur 1.18.1, but the resulting .list file doesn’t compute all of the distances. For one file, it stopped at 0.24. A smaller file stopped at 0.29. If I use mothur 1.15.0, distances up to 0.70 are computed.

I am fine with using 1.15.0 for now unless you know of any issues with using that version of mgcluster.

Billy Brazelton

The names file should not be needed. We will have to look into that. The change in distances outputted is most likely due to a change in the default clustering algorithm for version 1.18.1. The default was furthest and now it’s average.

Yes, you’re right. I specified method=average with version 1.15.0, and the distances stopped at 0.24. And I just realized for the first time that the .fn and .an extensions on the filenames refer to average neighbor and furthest neighbor! I always wondered about that…

I am having a hard time reproducing the sequence name issue you were having. Would you mind sending your blast file to

I could email you the file, but I get the error even when using the AMD.blast file I downloaded from