Hello! I am working on analysis of NHANES oral microbiome data for a class project. I am seeking to compare beta diversity across periodontal disease categories and across tooth loss categories. I have OTU files with read counts for ~5000 subjects in the periodontal disease analysis and ~7200 subjects in the tooth loss analysis. I also have separate metadata files that correspond to the OTU files via the unique subject identifiers issued by NHANES. I also have a csv file of the SILVA taxonomy used for annotation.
I have been able to calculate alpha diversities for these two analyses and run LEfSe analyses, but whenever I try to calculate beta diversities, there is a long computation time and then I receive a page indicating “an unknown error that is unique to your data and parameters.”
During the data filtering steps, I keep the default values for the low count and low variance filters. I do not perform any normalization.
I have uploaded my analysis files here for reference. Any assistance with this error would be much appreciated!