GNEISS. Aitchison basis is not orthonormal

[timanix (Timur Yergaliyev)]

Thank you for your answer!

@Nicholas_Bokulich

Could you please post the full command you used? This will help the gneiss developer trace your problem.

Of course. Here it is:

folders = ['All_Samples', 'No_Control', 'Control']
for folder in folders:
    Niche_list = ['Root', 'Gall', 'J2', 'Soil']
    for Niche in Niche_list:
        outdir    = '%s/By_Niche/%s/GNEISS'            % (folder, Niche)
        !mkdir $outdir
        
        table     = '%s/By_Niche/%s/%s_%s_table.qza'   % (folder, Niche, folder, Niche)
        hierarchy = outdir + '/%s_hierarchy.qza'       % Niche
        balances  = outdir + '/%s_balances.qza'        % Niche
        !qiime gneiss correlation-clustering \
            --i-table $table \
            --o-clustering $hierarchy
        !qiime gneiss ilr-hierarchical \
            --i-table $table \
            --i-tree $hierarchy \
            --o-balances $balances

@Nicholas_Bokulich

For now, my recommendation is to load your notebook in a 2019.1 environment and run with that. Some of the underlying packages that QIIME 2 uses for statistical analysis have been updated since the 2019.1 release, so there may be some backward incompatibility that needs to be addressed.

It was first I wanted to check.
I had Qiime2-2019.1 installed in anaconda2. Everything worked fine, I successfully performed GNEISS as described above. Then new release came out, I changed some filtration steps in the very beginning of the analysis so I decided to rerun my notebooks. But I wasn't able to install new release, constantly getting error as described here QIIME2 2018.4 Installation Error. Since I wanted to switch to anaconda 3 anyway I just deleted anaconda2, installed anaconda3 and new Q2 release. And got a mistake in GNEISS. As you suggested, I decided to repeat this step in Q2-2019.1, but again encountered an issue with installing Q2-2019.1 with the same error as here QIIME2 2018.4 Installation Error.
After running command from this answer QIIME2 2018.4 Installation Error - #9 by ebolyen I managed to install 2019.1 version.

Right now I am running the same command with GNEISS and it is working without errors. So maybe I found a bug.

Thanks again