bioconda qiime 1.9.1: make_otu_table produces binary biom file.

[Stefano]

Hello,
as in question title, is it right that make_otu_table (in conda environment) produces biom files in binary code?
We have three machines that have the same behaviour.
We need to operate on it with biom convert, add-metadata and so on...but the 'binary' biom seems not working...

With an older version of Qiime (1.8) the output of that command with the same input files is a 'text' format biom file.

Has anybody noticed this?

Thanks

stefano

[Stefano]

ok...i reply to myself:
the explanation is here:
https://github.com/joey711/phyloseq/issues/443

cheers,
stefano

[Colin Brislawn]

Yep. Qiime 1.9.1 produces .biom files in the HDF5 format (biom v2.1) . Phyloseq only supports .biom files in the json format (biom v1.0).

Eventually phyloseq will support the new .biom files.

https://github.com/joey711/biomformat/issues/1 

Colin