Organism rank print statements during annotation

[RRShieldsCutler]

When getting organism taxonomy from the ncbi tid

nt.green_genes_lineage(ncbi_tid, depth=8, depth_force=True)

DOJO prints each step of the rank to stdout. For example, for just one query:

['', '', '', '', '', '', 'Bifidobacterium_angulatum', 'Bifidobacterium_angulatum_DSM_20098_=_JCM_7096']
5
['', '', '', '', '', 'Bifidobacterium', 'Bifidobacterium_angulatum', 'Bifidobacterium_angulatum_DSM_20098_=_JCM_7096']
4
['', '', '', '', 'Bifidobacteriaceae', 'Bifidobacterium', 'Bifidobacterium_angulatum', 'Bifidobacterium_angulatum_DSM_20098_=_JCM_7096']
3
['', '', '', 'Bifidobacteriales', 'Bifidobacteriaceae', 'Bifidobacterium', 'Bifidobacterium_angulatum', 'Bifidobacterium_angulatum_DSM_20098_=_JCM_7096']
2
['', '', 'Actinobacteria', 'Bifidobacteriales', 'Bifidobacteriaceae', 'Bifidobacterium', 'Bifidobacterium_angulatum', 'Bifidobacterium_angulatum_DSM_20098_=_JCM_7096']
1
['', 'Actinobacteria', 'Actinobacteria', 'Bifidobacteriales', 'Bifidobacteriaceae', 'Bifidobacterium', 'Bifidobacterium_angulatum', 'Bifidobacterium_angulatum_DSM_20098_=_JCM_7096']

[bhillmann]

All the print statements have been removed. I fear our issue has to do with your 'root' conda environment and your other 'conda' environment are out of sync. The command

pip install git+https://github.com/knights-lab/DOJO.git --no-cache-dir --upgrade

Doesn't work to fix it.