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