UnicodeDecodeError: 'utf-8' codec can't decode byte 0x85 in position 28: invalid start byte

[paolamaragno]

Hello,

I created a conda environment where I successfully installed kneaddata 0.12.0, bowtie2 2.5.3, trf 4.09.1 and python 3.10.14.
However, I ran into this error when executing the command "kneaddata -un seq_fastq.zip --reference-db ./databases -t 15 --output ./output_dir":

Traceback (most recent call last):
File "/miniconda3/envs/meta_env/bin/kneaddata", line 8, in
sys.exit(main())
File "/miniconda3/envs/meta_env/lib/python3.10/site-packages/kneaddata/knead_data.py", line 480, in main
file_format=utilities.get_file_format(args.input[0])
File "/miniconda3/envs/meta_env/lib/python3.10/site-packages/kneaddata/utilities.py", line 552, in get_file_format
first_line = file_handle.readline()
File "/miniconda3/envs/meta_env/lib/python3.10/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x85 in position 28: invalid start byte

I tried different solutions proposed on the web but they didn't work. Do you have any suggestions?

Thank you very much,
Paola Maragno

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