TypeError: mkdir() got an unexpected keyword argument 'exist_ok' about duplex-tools HOT 5 CLOSED

Hi!

That's mysterious, Pathlib should have the exist_ok argument added from 3.5, and it looks like you're using 3.6.

Can you run this line below (swapping out python for the interpreter you're using if necessary)?

python -c "from pathlib import Path; Path('./output').mkdir(exist_ok=True)"

Let me know if that's giving the same error. You may want to try with python3.8 instead if it does.

from duplex-tools.

Thanks for your reply. I swapped out python for the python I used for duplex_tools and run the above command. It gave the same error.

Traceback (most recent call last): File "<string>", line 1, in <module> TypeError: mkdir() got an unexpected keyword argument 'exist_ok'

I will try with another python version. Thanks.

from duplex-tools.

Hi , @Rasinj
I reinstalled duplex_tools using python 3.8, run the same command : duplex_tools pairs_from_summary sequencing_summary.txt ./output , but the problem still exists.

[19:03:13 - FindPairs] Duplex tools version: 0.2.7
Traceback (most recent call last):
  File "/export/pipeline/RNASeq/Software/Duplex_tools/bin/duplex_tools", line 8, in <module>
    sys.exit(main())
  File "/export/pipeline/RNASeq/Software/Duplex_tools/lib/python3.8/site-packages/duplex_tools/__init__.py", line 39, in main
    args.func(args)
  File "/export/pipeline/RNASeq/Software/Duplex_tools/lib/python3.8/site-packages/duplex_tools/pairs_from_summary.py", line 336, in main
    find_pairs(
  File "/export/pipeline/RNASeq/Software/Duplex_tools/lib/python3.8/site-packages/duplex_tools/pairs_from_summary.py", line 34, in find_pairs
    outdir, output_pairs, output_intermediate = prepare_output_paths(
  File "/export/pipeline/RNASeq/Software/Duplex_tools/lib/python3.8/site-packages/duplex_tools/pairs_from_summary.py", line 101, in prepare_output_paths
    outdir.mkdir(parents=True, exist_ok=True)
TypeError: mkdir() got an unexpected keyword argument 'exist_ok'

from duplex-tools.

I checked my pathlib package version, it's 1.0.1. Is this version too old for duplex_tools?

but pip automatically installed pathlib 1.0.1 when I install duplex_tools.

Maybe the dependencies to install duplex_tools should be modified a little?

from duplex-tools.

Hi @defendant602, ah I think that must be it. Thanks for noticing. In fact, I believe it should be included by default, so perhaps the most sensible thing is to remove it as an explicit dependency

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