RESCRIPt: AttributeError: '_io.TextIOWrapper' object has no attribute 'rstrip'

Technical Support
13

Hi @kafker,

Thank you for your patience. The issue is indeed as @antias suggests: it is a (transient) issue with the latest versions (developer versions) of RESCRIPt and QIIME 2 that you have installed. The developer version has the get-gtdb-data action that you are using, but is not yet officially released and is not fully stable.

The solution:

  1. you can use the developer version for now to run get-gtdb-data but not evaluate-fit-classifier. Instead use qiime feature-classifier fit-classifier-naive-bayes.
  2. if you want to run evaluate-fit-classifier on the GTDB database, you must either (1) switch to another QIIME 2 environment and install an earlier tagged release (i.e., stable release version) of RESCRIPt or (2) wait another few weeks for when the 2023.5 stable release should be ready, then re-install RESCRIPt in a fresh QIIME 2 2023.5 environment. It should be fine to create the GTDB database files with the dev version of RESCRIPt, then switch to a non-dev environment to run evalute-fit-classifier.

Good luck!

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