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I am using the OBITools3 to try to analyze DNA metabarcoding data. I have had the same error come up multiple times when trying to run obi commands, such as obi taxonomy or obi alignpairedend. My code appears to be formatted correctly, and I don't know why I am getting the error! I'm using OBITools through a server at my university. I installed The OBITools 3 - Version 3.0.1b22 in a v-env with Python 3.6.8.

Here is the code I used to install OBItools

python3 -m venv new-env
source new-env/bin/activate
pip install --upgrade pip setuptools wheel Cython
pip install OBITools3

The code I tried to run:

obi alignpairedend --only 20 /data/student/td/R1.fastq -R /data/student/td/R2.fastq /data/student/td/OBIToolsTesting/ObiAligned.fastq

And the error info:

Traceback (most recent call last):
  File "/home/td/new-env/bin/obi", line 62, in <module>
    config[root_config_name]['module'].run(config)
  File "python/obitools3/commands/alignpairedend.pyx", line 133, in obitools3.commands.alignpairedend.run
  File "python/obitools3/uri/decode.pyx", line 177, in obitools3.uri.decode.open_uri
AttributeError: 'str' object has no attribute 'isascii'

I don't know much about Python, or virtual environments, and I can't figure out what the issue is, so any help is greatly appreciated! Would this be a version issue?

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  • The isascii() method of strings was added in Python 3.7, so it's not available to you with your current version. Commented Jul 27, 2023 at 21:07
  • @jasonharper I tried updating to python 3.7 (current version 3.7.12) but got the same error. Commented Jul 27, 2023 at 21:27

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