%s does not appear to be a BIOM file!

biom
(Michael Thon) #1

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??
THANKS!!!

(Justine) #2

Hi @Michael_Thon,

I think you’re try to convert from biom 1 ® to biom 2 (python).
If you’re doing a QIIME import, you can work from Biom 1 or Biom 2.

Best,
Justine