cluster.split output: list file+3empty temp files

Commands in mothur
1

Hi,

When running the cluster.split command with my bacteria 16S samples( mothur > cluster.split(fasta=Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=Undetermined.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table, taxonomy=Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, splitmethod=classify, taxlevel=4, cutoff=0.15)), I get the following output files:

  • Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list (10873 KB)
  • Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.36.dist (0KB)
  • Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.57.dist (0KB)
  • Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.69.dist (0KB)

During the process I see:

Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.36.dist is blank. This can result if there are no distances below your cutoff.
Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.36.dist is blank. This can result if there are no distances below your cutoff
Undetermined_trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.36.dist is blank. This can result if there are no distances below your cutoff

So I guess those files are not used for the clustering step later and that is why they remain there?

Does anybody know if it might be affecting the unique_list.list file or if I should use a different cutoff?

Thanks!

M

2

I think it’s probably fine, we’re just doing a bad job of cleaning up the files. If you run make.groups do you get any errors?

3

Hi Pat, Do you mean make.shared? I did not get any error with this command.

Thanks

4

right - make.shared - you’re good to go if there weren’t any errors.

pat

5

Great. Thank you!