h5py error in biom convert


i want to convert feature.biom file which i extracted from table.qza into a .tsv file so that i can view otu reads in excel. i run the code below.

biom convert -i feature-table.biom -o table.tsv --to-tsv

after i got this error “RuntimeError: h5py is not installed, cannot parse HDF5 BIOM file” i installed h5py but im still getting the same error. restarting the terminal didnt work either. i couldnt find a topic about this or another way to create a .tsv, so i need a little help here.

thank you for your attention…

Hello @the_dummy,

What version of Qiime2 are you using, and how are you using it (virtual machine, conda install on your local machine, hpc, etc.)?

Thank you.


im using conda on my local machine and i have 2019.4 and 2019.7. now that you mentioned it, i tried 2019.4 and it worked!! i had a problem with 2019.7 some time ago. seems like something went wrong with installation so i will try reinstalling it.

thank you very much!!

1 Like