mothur

Make.biom: bug or user error?

Dear all,

I have a taxonomy table which I’m trying to convert to biom, with make.biom. Since I made the table outside of mothur, I mimicked the example provided, converting my table into a shared and a taxonomy file and tried using make.biom with constaxonomy command. However, from my 14 samples, only the first gets converted to biom, with only its 2.2k OTUs instead of all samples with ~3.7k OTUs. Am I missing something?

Here is a snipet of my table:

Many thanks for the attention,
Best regards,
Gustavo

Hi Gustavo,

It looks like you have 16 samples, not 14. Also, the values in the numOtus column should all be the same - it is the number of columns that follows the nuOtus column. Could you try edting that and give it another shot?

Pat

Perfect. That nailed it. Somehow I thought richness was necessary instead of maximum OTU number. Easily corrected and the biom was produced right this time. Thanks for the tip! All the best!

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