make.biom with picrust parameter

Commands in mothur
1

Hello -

I’m attempting to ‘make.biom’ with the following command:
mothur > make.biom(shared=merged.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.shared, label=0.03, constaxonomy=merged.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.taxonomy, reftaxonomy=gg_13_5_99.gg.tax, picrust=97.gg.otu_map).

I’ve read probably all the posts on the forum and attempted nearly everything, however I still get this error: [ERROR]: could not find OTUId for k__Bacteria(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);k__Bacteria_unclassified(100);. Its reference sequences are .

Yes I used the greengenes db for classifying sequences and otus… have tried current and older dbs and mapping tables. And I don’t think its particularly accurate to just delete OTUs that aren’t classified as one poster suggested in another thread… if the unclassified OTUs are the problem.

Please help.

2

Have you modified any of the files outside of mothur?

3

Hello,

I did try exactly the same as described here and received the same error message. I did not modify any of the files outside of mothur. Did you already find a solution for this issue?

Cheers, Leo

4

I’m sorry for missing the information in the “MOTHUR bugs” part of the forum dealing with this issue (Make.biom picrust option doesnt handle unclassified?). That helped me a lot!