problems with .names or .fasta files while using cluster

I am triying to use cluster command after using split.abund and dist.seqs, with my .abund fasta and names files, but when I run it I get a message saying that many sequences are missing form one of them (.fasta or .names).

Am I using the wrong files?

Here is my commands sequence:

cluster(name=bacpia0.trim.unique.good.filter.unique.precluster.abund.names, method=furthest)


as far as I see it you are missing part of the necessary Cluster parameters, i.e. don´t provide the column- or phylip-formatted distance matrix. Have a look at the CLUSTER command in the wiki. Try the distance matrix you get from the dist.seqs command like this:
cluster(column=bacpia0.trim.unique.good.filter.unique.precluster.pick.abund.dist, name=bacpia0.trim.unique.good.filter.unique.precluster.abund.names, method=furthest)

Good luck!

Did you give split.abund the right files? It looks like your fasta has a “pick” in it and the names file does not.


Before this commands I have run a chimera.uchime and a remove.seqs. In this latter I haven’t removed seqs from the .names file, so I am trying to do that and see If it generates the .names file required to my cluster command

I think that I have fixed the problem this way, you were right. It was a problem with the files.

Thanks a lot