This is the output of the biom format using the mothur tool.
stability.opti_mcc.0.03.subsample.0.03.biom.gz
However, this was not suitable for the phinch input format.
So I fount a similar issue. (#48)
And I used the following two codes.
biom convert -i stability.opti_mcc.0.03.subsample.0. 03.biom -o file-for-phinch.biom --table-type="OTU table" --to-json
sed -i 's#null#{}#g' file-for-phinch.biom
But still phinch did not work.
So we changed null to [] as #82
But it still does not work.