problem with classify.otu

mothur bugs
1

Hi,
I have the same problem classify.seqs error in mothur-1.22
I use mothur v.1.37.2

When I used classify.otu command I received this error:

mothur > classify.otu(taxonomy=fool.unique.filter.precluster.pick.silva.wang.pick.taxonomy, list=fool.unique.filter.precluster.pick.pick.phylip.an.list, name=fool.unique.filter.precluster.pick.pick.names, group=fool_group.pick.pick.groups, reftaxonomy=silva.tax, label=0.03-0.06-0.10-0.15-0.20-0.25, cutoff=80, basis=sequence)
0.03 7365
Warning: cannot find taxon LD12_freshwater_group_unclassified in reference taxonomy tree at level 5 for Tih1_10051. This may cause totals of daughter levels not to add up in summary file.
Warning: cannot find taxon LD12_freshwater_group_unclassified in reference taxonomy tree at level 5 for Tih1_14125. This may cause totals of daughter levels not to add up in summary file.
Warning: cannot find taxon LD12_freshwater_group_unclassified in reference taxonomy tree at level 5 for Tih1_14828. This may cause totals of daughter levels not to add up in summary file.
…etc.


below is a part of *.summary file

5 0.2.16.1.7.5 Rickettsiales_unclassified 1 8
6 0.2.16.1.7.5.1 Rickettsiales_unclassified 0 8
5 0.2.16.1.7.6 SM2D12 1 4
6 0.2.16.1.7.6.1 SM2D12_unclassified 0 4
4 0.2.16.1.8 SAR11_clade 2 8047
5 0.2.16.1.8.1 LD12_freshwater_group 1 8035
6 0.2.16.1.8.1.1 LD12_freshwater_group_unclassified 0 8035
5 0.2.16.1.8.2 Surface_1 1 12
6 0.2.16.1.8.2.1 Surface_1_unclassified 0 12
4 0.2.16.1.9 Sphingomonadales 4 410
5 0.2.16.1.9.1 7B-8 1 1
6 0.2.16.1.9.1.1 7B-8_unclassified 0 1
5 0.2.16.1.9.2 SWB04 1 1
6 0.2.16.1.9.2.1 SWB04_unclassified 0 1


When I used mothur v. 1.35.1 I didn't have this error. I hope anybody could help me with it... Thanks!
2

Can you try our current version, https://github.com/mothur/mothur/releases/tag/v1.37.4?

3

I tried. There was the same error :frowning:

4

Running the command without the reftaxonomy parameter will remove the error. It will not effect the results of the classification or the create.database command. Removing the reftaxonomy parameter will cause the rankIDs in the tax.summary file will be regenerated instead of matching those in the classify.seqs command. If you don’t use the rankIDs in the *.tax.summary file, but instead use the taxon names, you don’t need the reftaxonomy parameter. Thanks for reporting this bug!