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iu-trim-fastq not working #29

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FlorianTrigodet opened this issue Jul 26, 2021 · 3 comments
Closed

iu-trim-fastq not working #29

FlorianTrigodet opened this issue Jul 26, 2021 · 3 comments
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@FlorianTrigodet
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Using v2.10.
I've tried to use iu-trim-fastq but it failed with this error:

iu-trim-fastq -f 0 -t 100 R1.fastq.gz R1-TRIMMED-TO-100bp.fastq.gz
 00% -- (num pairs processed: 1) Traceback (most recent call last):
  File "/project2/meren/VIRTUAL-ENVS/anvio-dev/bin/iu-trim-fastq", line 51, in <module>
    sys.exit(main(input_file_path, output_file_path, args.trim_from, args.trim_to, compressed))
  File "/project2/meren/VIRTUAL-ENVS/anvio-dev/bin/iu-trim-fastq", line 25, in main
    output.store_entry(input.entry)
  File "/project2/meren/VIRTUAL-ENVS/anvio-dev/lib/python3.6/site-packages/IlluminaUtils/lib/fastqlib.py", line 191, in store_entry
    self.file_pointer.write('@' + e.header_line + '\n')
  File "/project2/meren/VIRTUAL-ENVS/anvio-dev/lib/python3.6/gzip.py", line 260, in write
    data = memoryview(data)
TypeError: memoryview: a bytes-like object is required, not 'str'

Maybe related to a python 2 to 3 migration?
Thanks for the help!

@meren meren self-assigned this Jul 29, 2021
@meren meren closed this as completed in cd87a73 Jul 29, 2021
meren added a commit that referenced this issue Jul 29, 2021
@meren
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meren commented Jul 29, 2021

This should be fixed now. I will make a release so you can update it via pip.

@meren
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meren commented Jul 29, 2021

Done. You should be able to pip install --upgrade illumina-utils now :)

@meren
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meren commented Jul 29, 2021

The version you're looking for is v2.12

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