mothur

Warning notice from classify.otu


#1

When trying to find a consensus taxonomy for each OTU, and using the classify.otu command I received a few dozen of the following warnings:

“[WARNING]: M01625_91_000000000-D3MRR_1_1102_21759_7731 is not in your taxonomy file.
I will not include it in the consensus.”

Is this something I should be worried about?


#2

Hi luker,

Yeah, that might be a problem. You need to make sure that you are using the right files. Can you post the classify.otu and upstream commands as you are running them?

Pat


#3

Hi Pat,

Very grateful for your response.

I’ll copy in my workflow from the clustering sequences into otus stage:

dist.seqs(fasta=current, cutoff=0.03)

Using PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta as input file for the fasta parameter.

It took 79 secs to find distances for 8928 sequences. 96279 distances below cutoff 0.03.

Output File Names:
PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.dist

cluster(column=PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.dist, count=PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table)

Output File Names:
PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.list
PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.steps
PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.sensspec

make.shared(list=PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.list, count=PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table, label=0.03)

Output File Names:
PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.shared

classify.otu(list=PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.list, taxonomy=PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.pick.taxonomy, count=current, label=0.03)

[WARNING]: M01625_91_000000000-D3MRR_1_1102_21759_7731 is not in your taxonomy file. I will not include it in the consensus. etc. etc.

Output File Names:
PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.0.03.cons.taxonomy
PV4.fish.ponds.test.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.0.03.cons.tax.summary

Any ideas? :slight_smile: