Error occurred on running autometa-binning

[chtsai0105]

Current Behavior

Steps to Reproduce

An error occurred immediately while running autometa-binning step when installed from conda/mamba.

$ mamba create -n autometa autometa=2.1.0
$ conda activate autometa
$ autometa-binning

Traceback (most recent call last):
  File "/home/chtsai/miniconda3/envs/autometa/bin/autometa-binning", line 7, in <module>
    from autometa.binning.recursive_dbscan import main
  File "/home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/binning/recursive_dbscan.py", line 20, in <module>
    from hdbscan import HDBSCAN
  File "/home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages/hdbscan/__init__.py", line 1, in <module>
    from .hdbscan_ import HDBSCAN, hdbscan
  File "/home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages/hdbscan/hdbscan_.py", line 509, in <module>
    memory=Memory(cachedir=None, verbose=0),
TypeError: __init__() got an unexpected keyword argument 'cachedir'

Expected Behavior

Expected to see the help page.

Environment Information

autometa-config --print

Not sure what happening...

[09/17/2022 11:42:50 PM INFO] autometa.config.utilities: Updating default.config ([common],home_dir): /home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages
[09/17/2022 11:42:50 PM DEBUG] autometa.config.utilities: updated /home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/config/default.config [common] option: home_dir : /home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages
Traceback (most recent call last):
  File "/home/chtsai/miniconda3/envs/autometa/bin/autometa-config", line 10, in <module>
    sys.exit(main())
  File "/home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/config/utilities.py", line 237, in main
    cfg, environ_satisfied = environ.configure(cfg)
  File "/home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/config/environ.py", line 265, in configure
    versions = get_versions()
  File "/home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/config/environ.py", line 229, in get_versions
    version = get_version()
  File "/home/chtsai/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/config/environ.py", line 148, in bowtie2
    return stdout.decode().split()[2]
IndexError: list index out of range

Possible solution

Actually I've run 2.1.0 version successfully before. I compared the previous build and current build and found that the package joblib have been updated recently. (1.1.0 -> 1.2.0) I downgraded the joblib to 1.1.0 and everything is good now. Maybe have to look into what was changed in the newer joblib update or simply pin the joblib to 1.1.0.

[evanroyrees]

Hello @chtsai0105, I believe this is an issue we've previously encountered.

Issue: #285 -> PR: #286

Good to know that downgrading joblib also fixes the issue.

[chtsai0105]

Thank you Evan! Since there is already a fix, I'm closing this issue.