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:
split.abund(cutoff=1)
dist.seqs(fasta=bacpia0.trim.unique.good.filter.unique.precluster.pick.abund.fasta)
cluster(name=bacpia0.trim.unique.good.filter.unique.precluster.abund.names, method=furthest)
get.oturep()
Hi,
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.
fasta=bacpia0.trim.unique.good.filter.unique.precluster.pick.abund.fasta
name=bacpia0.trim.unique.good.filter.unique.precluster.abund.names
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