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?
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
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? 