Fungi taxonomic analysis

I ran into this problem and found two options that work. If you want to run the trained classifier you already have, you can activate an older version of qiime2, for example, I think 2019.7 works because it has the older scikit-learn version. But it sounds like you were already able to get that version installed, so if you try to run it with your older classifier, I think it should work. (Edited: Sorry, I just reread the thread and saw you are getting an error running your old classifier, so this probably won’t actually work, but try the steps below)

If you want to use the new database you just downloaded, you are correct that it needs to be a .qza object. When you download it, it comes as a .gz file, so first you need to extract it. I use 7-zip on a Windows machine, and I used the “Extract Here” command once to get rid of the .gz and then again to extract a folder that has the files you need - fasta and txt files. In the command line interface, I think you can use the gunzip command but I’m not sure.

Then run these commands:

nohup qiime tools import
–type ‘FeatureData[Sequence]’
–input-path sh_refs_qiime_ver8_dynamic_s_02.02.2019.fasta
–output-path sh_refs_qiime_ver8_dynamic_s_02.02.2019.qza &

nohup qiime tools import
–type ‘FeatureData[Taxonomy]’
–input-format HeaderlessTSVTaxonomyFormat
–input-path sh_taxonomy_qiime_ver8_dynamic_s_02.02.2019.txt
–output-path sh_taxonomy_qiime_ver8_dynamic_s_02.02.2019.qza &

nohup qiime feature-classifier fit-classifier-naive-bayes
–i-reference-reads sh_refs_qiime_ver8_dynamic_s_02.02.2019.qza
–i-reference-taxonomy sh_taxonomy_qiime_ver8_dynamic_s_02.02.2019.qza
–o-classifier sh_classifier_qiime_ver8_dynamic_s_02.02.2019.qza &

Those commands might change a little depending on which database version you downloaded. I used this one - https://doi.org/10.15156/BIO/786387. If you downloaded a different one, you won’t have the s after ‘dynamic’ in the file names.

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My mistake - I just reread the thread and saw you’re still getting a “not a Qiime2 artifact” error with your old classifier and your sequence/taxonomy files. I’m not sure what’s causing that.

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Thanks @lzgles - your answer is the “correct” one amongst this thread.

I think that the error @elolimy describes above is caused by their QIIME 2 conda environment becoming corrupted by adding and removing packages.

@elolimy - please remove your conda env, start fresh with a new 2020.6 installation. Then, follow the excellent directions that @lzgles has provided.

:qiime2:

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Thanks @thermokarst! Do you think if I uninstalled my current version of Qiime and install the older one for 2019.7 my issue will be fixed? Do I also need to install an older version of conda environment or the older Qiime should be enough and will take care of it?

Yes, although I’m not sure which version of QIIME 2 you need - as long as you’re running the same version of QIIME 2 used to train the classifier, you’ll be fine.

I don’t understand the question - the “older QIIME” is installed using a conda environment - the two things are one and the same.

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