Error with cluster.split from MiSeq SOP

Hi everyone,

I am running Mother 1.39.1

When I run the cluster.split command as shown in the MiSeq SOP

mothur > cluster.split(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table,, splitmethod=classify, taxlevel=4, cutoff=0.03)

I get the following error:

NOTE]: Default clustering method has changed to opti. To use average neighbor, set method=average.
[ERROR]: did not complete cluster.split.

I looked at the cluster.split pages and there seem to be many options but I’m confused about which command I should run, any help would be swell?

Hey gkuffel,
In my opinion the command is ran correctly, you might want to check the Mothur version you are using since there were several improvements to the cluster method and other commands until the last one, 1.39.5


I believe the command is incorrect in the MiSeq SOP. If I change the splitmethod to “opti” I don’t get the error.

Please upgrade to 1.39.5 - there was a minor bug related to this issue that was addressed.


I’m also having this problem and I have updated to mothur 1.39.5

I am not able to reproduce a problem with 1.39.5. Could you be accidentally using an older version of mothur?