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  • #121

Closed
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Opened Apr 05, 2022 by CHRISTINE CHIVAS@christine.chivas

Issue with obi import

Good afternoon I am trying to use the import function using the following command and am receiving the following error

obi import --embl EMBL reference_sequences/embl_refs

2022-04-04 15:16:30,261 [import : INFO ] obi import: imports an object (file(s), obiview, taxonomy...) into a DMS Traceback (most recent call last): File "/scratch/fb14/cc8881/obi3-env/bin/obi", line 62, in config[root_config_name]['module'].run(config) File "python/obitools3/commands/import.pyx", line 144, in obitools3.commands.import.run File "python/obitools3/uri/decode.pyx", line 177, in obitools3.uri.decode.open_uri AttributeError: 'str' object has no attribute 'isascii'

I am receiving the same error regardless of what I am trying to import (EMBL ref sequences, tax dump, FASTQ file). I have trialled importing a subset of these files using obitools running off my computer rather then the server and have had no issues. I'm currently running obitools version 3.0.1b16 and python 3.10.0

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Reference: obitools/obitools3#121