create.database missing names

Commands in mothur
1

Hi,

I am trying to used the create.database command with the count file options on a normalized dataset, but I have an error saying that my repnames does not match. However, I am not using that as an input, so I do not know how to correct for it since I have not touched the names file since my first trim.seqs command. I am not sure what I am missing here!

Thanks!

Commands:
make.shared(list=current, count=current, label=0.03)
count.groups()
sub.sample(list=current, count=current, size=166)
classify.otu(list=current, count=current, taxonomy=current, label=0.03)
get.oturep(list=UQ_all.trim.unique.good.filter.unique.precluster.pick.an.unique_list.subsample.list, label=0.03, fasta=UQ_all.trim.unique.good.filter.unique.precluster.pick.fasta, column=UQ_all.trim.unique.good.filter.unique.precluster.pick.dist, count=UQ_all.trim.unique.good.filter.unique.precluster.uchime.pick.count_table)
create.database(list=UQ_all.trim.unique.good.filter.unique.precluster.pick.an.unique_list.list, label=0.03, repfasta=UQ_all.trim.unique.good.filter.unique.precluster.pick.an.unique_list.0.03.rep.fasta, count=UQ_all.trim.unique.good.filter.unique.precluster.pick.an.unique_list.0.03.rep.count_table, contaxonomy=UQ_all.trim.unique.good.filter.unique.precluster.pick.an.unique_list.0.03.cons.taxonomy)

Error:
Using UQ_all.trim.unique.good.filter.unique.precluster.pick.an.unique_list.subsample.list as input file for the list parameter.
[ERROR]: you have 835 unique seqs in your repname file, but 76 seqs in your repfasta file. These should match.

2

Thanks for reporting this issue. We have a bug with in the get.oturep command with the count file. It will be fixed in our next release coming very soon.

3

I have updated to mothur v.1.33.3, but I am still having this issue. I am not able to follow the complete set of commands pasted below on subsampled versions, without getting the same error I was having before:

mothur > get.oturep(list=final.an.unique_list, label=0.03, fasta=final.fasta, column=final.dist, count=final.count_table)
mothur > classify.otu(list=final.an.unique_list, count=final.count_table, taxonomy=final.taxonomy, label=0.03)
mothur > create.database(list=final.an.unique_list, label=0.03, repfasta=final.an.0.03.rep.fasta, count=final.an.0.03.rep.count_table, constaxonomy=final.an.0.03.cons.taxonomy)