Mothur Classify OTU Problems

[albreaks]

Hello,

I keep coming across an issue at the classify OTU step.

The label is set at 0.03 to determine a 97% similarity between OTUS.
After I run the command mothur output says "Your file does not include the label 0.03. I will find the next smallest label 0.16"
This set alls of my data to 84% similarity.

Has anyone experienced this issue before?
Do you know why the label would not work?
Does it have to do with the SILVA file folder I have to use for the taxonomy?

Any responses are helpful.
Thanks!

Ashlee

[thermophile]

Without knowing anything about your samples or commands run, it's not possible to help. The mothur forum is pretty active, I suggest looking through that and potentially posting there if you can't find an answer.

[jpummil]

Ashlee,

Can you post the command that specifies 0.03?

I wonder if the 0.03 requires a unique processing step back a few more commands to appropriately set your data correctly for the 0.03 you mention to work?

[albreaks]

The command is as follows:
classify.otu(list=rumenAB.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.unique_list.list, count=rumenAB.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, taxonomy=rumenAB.trim.contigs.good.unique.good.filter.unique.precluster.pick.rdp.wang.pick.taxonomy, label=0.03)

[thermophile]

go to the mothur forum and explain in more detail what your samples are, sequenced region, etc along with all commands

https://www.mothur.org/forum/index.php

[albreaks]

Thank you for the help!