Dear Sean and Christian,
I’m very curious about micom and I tested it as a new plugin for qiime2. However, I experienced several issues:
First I tried to apply the tool on my own example dataset, but received the following error with the qiime micom build command:
Plugin error from micom: Length mismatch: Expected axis has 15 elements, new values have 8 elements
Ok then I thought I should stick to your example data covered in your tutorial (q2-micom/README.md at master · micom-dev/q2-micom · GitHub)
However, for the crc_table.qza and crc_taxa.qza files I received the following error with qiime micom build:
(1/2) Invalid value for “–i-abundance”: ‘crc_table.qza’ is not a QIIME 2
(2/2) Invalid value for “–i-taxonomy”: ‘crc_taxa.qza’ is not a QIIME 2
Hm, then I thought let’s try the small dataset of the moving picture tutorial (“Moving Pictures” tutorial — QIIME 2 2019.10.0 documentation) and the qiime micom build command worked!
Nevertheless, with the qiime micom grow command I got another error:
Plugin error from micom: ‘NoneType’ object is not subscriptable
I guess this was due to several warnings I received during the execution that qiime micom grow could not solve cooperative tradeoffs for many samples.
So I was wondering how to proceed from here. Would be great if you could comment on those errors or maybe check the artifacts of the crc files, or recommend other suitable test datasets to get an idea how to get micom work…
By the way I used qiime2 2019.10 and the gurobi license.
Thanks for any support!