I am trying to assign taxonomy to my 16S samples using QIIME 2 version 2022.2 (and the SILVA 138 database release), but I received the "Plugin error from feature-classifier: pop from empty list" error when I ran the qiime feature-classifier classify-sklearn command:
The error does not show up when I include the --p-confidence=disable option, but as per this post, I know it would be better to not use this option.
Numerous previous posts indicate this error means there is an issue with the classifier file. This post says an incomplete taxonomy will generate the error; however, I made my classifier file by following the RESCRIPt tutorial to create a consensus taxonomy, using the 'lca' option:
To my understanding, this command will fill empty lower-level taxonomy with empty place-holders. I confirmed that these place-holders were included in my file by visualizing my reference taxonomy file with this command:
Do you have any suggestions for what may be causing the error I am seeing? Perhaps there is still an issue with my classifier file, although I am not sure what that issue is. I would be happy to provide any necessary files for help with troubleshooting.
Thank you for your help; it is greatly appreciated!
Thank you so much for your response! The problem was that I was trying to use the dereplicate lca mode with more than the 7 standard taxonomy ranks. I fixed this problem by taking your advice and using the uniq mode instead:
Thanks for responding! As you can see from the other topic discussion, we have an open ticket to add support for more than 7 ranks, so this feature should be available some time in the future (contributions to the source code are welcome )