Running an example

[nzarnaghi]

Hi,

I want to run the example provided below:

mmvec paired-omics
--microbe-file examples/cf/otus_nt.biom
--metabolite-file examples/cf/lcms_nt.biom
--summary-dir summary

But after running these commands, it shows the following error at the end:

TypeError: SparseDataFrame() takes no arguments

In addition, when I run tensorboard --logdir . , it shows the following error at the end:

ValueError: Duplicate plugins for name projector

Could you please guide me what might be the problem?

[mortonjt]

It looks like pandas 1.0 has made some breaking changes to biom. See here: biocore/biom-format#837

The solution for now is to run
conda install pandas<1.0

Just merged in a PR here: conda-forge/mmvec-feedstock#7
So a more permanent solution is in the works

[nzarnaghi]

Hi

Thank you so much. I tried

conda install pandas<1.0

But now, it shows this error:

bash: 1.0: No such file or directory

[mortonjt]

Sorry, that was a typo - that should be conda install pandas=0.24

But the conda install should be working now, so feel free to retry the original install instructions.

[nzarnaghi]

Thank you so much. It worked now.

[mortonjt]

great!