AttributeError: module 'urllib' has no attribute 'parse'

[korjent]

Hi Edgar,

Quick question, I have upgraded to Captus 1.6 and am getting this error. Any suggestions?
I am working on an HPC at Adelaide University.

Cheers

Kor

HybCap135_extract_Captus_6231892.log

[edgardomortiz]

Hi Kor,

Try this solution, somebody recently found a similar error. In short, I recommend re-doing the extraction or adding --overwrite to the command:

#31

Edgardo

[korjent]

Thank you for your quick reply!
Just tried, but no luck, same error.

Kor

[edgardomortiz]

OK, let's figure it out. Did you try from scratch or adding --overwrite?
Could you send me the new log with the error please? and also the file captus-extract.log from inside the extraction folder.

Edgardo

[korjent]

Yep, I cleaned everything up and added --overwrite. I even made a new environment and started clean.
Not had trouble in the past..

Hope you find something useful.

captus-extract.log

HybCap135_extract_Captus_6232268.log

[edgardomortiz]

Interesting, it seems that conda installed the most recent Python 3.14! I will have to fix Captus after testing this new version. In the meantime please create a new environment for Captus 1.6.0 and Python 3.13 as follows:

conda (or mamba) create -n captus160 -c bioconda -c conda-forge captus python=3.13

Let me know if this works,

Edgardo

[korjent]

Maybe problem is related to this error:

[a1638383@p2-log-1 HybCap135]$ conda create -n captus160 -c bioconda -c conda-forge captus python=3.13
Channels:

• bioconda
• conda-forge
• defaults
  Platform: linux-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• package captus-1.5.4-pyh05cac1d_0 requires clipkit, but none of the providers can be installed

Could not solve for environment specs
The following package could not be installed
└─ captus =* * is not installable because it requires
└─ clipkit [=* *|>=1.3.0 *], which requires
└─ tqdm >=4.45.0 *, which conflicts with any installable versions previously reported.

[edgardomortiz]

Sometimes I hate conda, I have just tried this command and it works:

mamba create -n captus_test_160 -c bioconda -c conda-forge python=3.13 captus

Maybe placing python before captus made the difference? I am using mamba 2.0.7 and conda 25.5.0 from the miniforge distribution on a Linux HPC by the way...

Edgardo

[korjent]

Tried with mamba:

[a1638383@p2-log-1 HybCap135]$ mamba create -n captus_test_160 -c bioconda -c conda-forge python=3.13 captus
warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.

warning libmamba Please make sure you understand Anaconda Terms of Services.

warning libmamba See: https://legal.anaconda.com/policies/en/
bioconda/noarch 5.0MB @ 9.5MB/s 0.5s
bioconda/linux-64 5.3MB @ 8.6MB/s 0.6s
pkgs/main/linux-64 8.5MB @ 7.9MB/s 0.7s
conda-forge/noarch 22.7MB @ 18.5MB/s 1.1s
conda-forge/linux-64 47.7MB @ 31.8MB/s 1.4s

warning libmamba The specification of the environment does not seem solvable in your current setup.
warning libmamba For instance, packages from different channels might be specified,
warning libmamba whilst your current configuration might not allow their resolution.
warning libmamba
warning libmamba If it is the case, you need to either:
warning libmamba - adapt the channel ordering (e.g. by reordering the -c flags in your command line)
warning libmamba - use the flexible channel priority (e.g. using --channel-priority flexible in your command line)
warning libmamba
warning libmamba For reference, see this piece of documentation on channel priority:
warning libmamba https://docs.conda.io/projects/conda/en/stable/user-guide/tasks/manage-channels.html#strict-channel-priority
error libmamba Could not solve for environment specs
The following package could not be installed
└─ captus =* * is not installable because it requires
└─ clipkit [=* *|>=1.3.0 *], which requires
└─ tqdm >=4.45.0 *, which conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specs

[korjent]

Sorry for being such a pain..
I am a user, not very articulate in bioinformatics..

[edgardomortiz]

No worries, conda has given me many headaches as well. Sometimes I just delete the entire conda installation and start fresh. Try cleaning the cache of conda first:

conda clean --all

Another option is, if you have an environment with a previous Captus that works, activate it and update only Captus with:

conda update -c bioconda captus

[korjent]

Success!
conda clean didn't do anything.
But updating my v1.3 did do the trick.

Thank you for being so helpful

[edgardomortiz]

Excellent! I'm glad you could solve it. Did you try running the extraction already?

[korjent]

Yes, it is a very simple extraction. I will now add to it and also do the clustering.

[edgardomortiz]

Nice, let's keep the issue open in case other people get the same error...

[bmichanderson]

Hi guys, just adding that I hit the same error running a recent extraction. The extractions worked in serial (using --debug), but the parallel job dies after a few minutes:

concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
  File "/opt/conda/envs/captus_env/lib/python3.14/concurrent/futures/process.py", line 254, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/opt/conda/envs/captus_env/lib/python3.14/site-packages/captus/extract.py", line 1686, in scipio_coding
    write_gff3(
    ~~~~~~~~~~^
        final_models,
        ^^^^^^^^^^^^^
    ...<3 lines>...
        Path(yaml_final_dir, f"{marker_type}_contigs.gff"),
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/opt/conda/envs/captus_env/lib/python3.14/site-packages/captus/bioformats.py", line 3683, in write_gff3
    source = urllib.parse.quote("Captus (Scipio)")
             ^^^^^^^^^^^^
AttributeError: module 'urllib' has no attribute 'parse'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/conda/envs/captus_env/bin/captus", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "/opt/conda/envs/captus_env/lib/python3.14/site-packages/captus/captus_assembly.py", line 1562, in main
    CaptusAssembly()
    ~~~~~~~~~~~~~~^^
  File "/opt/conda/envs/captus_env/lib/python3.14/site-packages/captus/captus_assembly.py", line 86, in __init__
    getattr(self, args.command)()
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/opt/conda/envs/captus_env/lib/python3.14/site-packages/captus/captus_assembly.py", line 1167, in extract
    extract(full_command, args)
    ~~~~~~~^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/captus_env/lib/python3.14/site-packages/captus/extract.py", line 621, in extract
    tqdm_parallel_nested_run(
    ~~~~~~~~~~~~~~~~~~~~~~~~^
        scipio_coding,
        ^^^^^^^^^^^^^^
    ...<5 lines>...
        args.show_less,
        ^^^^^^^^^^^^^^^
    )
    ^
  File "/opt/conda/envs/captus_env/lib/python3.14/site-packages/captus/misc.py", line 165, in tqdm_parallel_nested_run
    result = future.result()
  File "/opt/conda/envs/captus_env/lib/python3.14/concurrent/futures/_base.py", line 443, in result
    return self.__get_result()
           ~~~~~~~~~~~~~~~~~^^
  File "/opt/conda/envs/captus_env/lib/python3.14/concurrent/futures/_base.py", line 395, in __get_result
    raise self._exception
AttributeError: module 'urllib' has no attribute 'parse'