in R I used the library biomformat and the function write_biom() to save biom data to a file. The file appears to be json. I tried to convert it to a table using this command:
biom convert -i out/CSS_normalized_table.biom -o out/feature-table-collapsed-rel-freq.tsv --to-tsv
but I get this error:
raise TypeError("%s does not appear to be a BIOM file!" % f)
Does anyone know why??