I am running the tax-credit-code for taxonomy assignment of naive-bayes command (following the exact code in the taxonomy-assignment-naive-bayes-commands.ipynb notebook). I have double-checked my paths and everything seems to run fine except at the very end where I am unable to generate any "taxonomy.tsv" files using the naive-bayes commands I generated, and I am getting all "bad-classifications". I wonder if anyone has run into the same issue.
Hi @mcosele ,
I am reclassifying this post as "other bioinformatics tools" as this concerns the tax-credit repositories, and not QIIME 2 specifically. Any issues with those repositories should be opened as an issue there and not on the QIIME 2 forum.
The tax-credit repositories are quite out of date at this point and are very likely broken in a few places (where breaking changes have been made to QIIME 2 or other packages) so this is most likely leading to the error messages. I recommend running QIIME 2 directly at this point instead of using tax-credit for benchmarking (or otherwise significantly updating that notebook to fix any outdated parameter names/settings).
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