Hello, I'm self-studying microbial analysis and encountered an error during the process. The command I used and the error that occurred are as follows:
qiime feature-classifier classify-sklearn --i-classifier /root/Qiime2/04_taxonomy/silva-138-99-nb-classifier.qza --i-reads /root/Qiime2/02_Denoising/rep-seq.qza --o-classification /root/Qiime2/04_taxonomy/taxonomy.qza
Even with the latest Silva database, the Qiime2 version, and reinstalling Qiime2, the same error persists.
Welcome to the forums, Jung. 
These are all good ideas and, because that did not help, they give us a clues to the source of the error.
The error 'unexpected end of data' would happen if a file download is incomplete. One of the .qza files is messed up/incomplete.
If you have already downloaded a new copy of the silva classifier, try redownloading or remaking the rep-seq.qza file.
Hello,
I created a new rep-seq.qza file, but the error still appeared the same. Still, I'm really grateful for your help with the new approach!!
Great!
Can you also download a new copy of the silva classifier .qza from the Data Resources Page:
https://docs.qiime2.org/2024.2/data-resources/
When you rerun the command with the newly downloaded classifier, please add the --verbose flag because that will give us even more clues!
I appreciate your dedication to try all these things, especially within a self-study context.
Good work!
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