make.shared (biom) -> venn()


I want to use the command make.shared (biom=) to convert my QIIME .biom file to MOTHUR’s .shared file, which eventually will be used to do up a Venn Diagram with the venn() command.

Previously I was using v1.31, which I assumed was the problem so I downloaded MOTHUR v1.34 as I understand that the make.shared(biom=) command was upgraded in this version.

However, I got the following message in the log file at the first command :
mothur > make.shared(biom=./open_otus/otu_table_mc2_w_tax.biom)
[ERROR]: 3.0 has occurred in the MothurOut class function mothurConvert.

My question(s) are :

  1. Do I need to uninstall my v1.31 to let v1.34 work optimally ?

  2. Is my planned workflow correct, ie to convert .biom -> .shared -> venn() ?

I look forward to your advice.


Looking at the error message you are getting, I suspect your biom file contains abundances that are not integers. If your matrix_element_type is set to integer, change this to float. If this does not resolve the issue, then you can send me your biom file at and I will take a closer look.