atlas: Error in rule dram_download

• I checked and didn’t found a related issue,e.g. while typing the title
• ** I got an error in the following rule(s)😗* dram_download
• I checked the log files indicated indicated in the error message (and the cluster logs if submitted to a cluster)

Error in rule dram_download:
    jobid: 409
    output: [...]dat/db/atlas/DRAM/db, [...]dat/db/atlas/DRAM/DRAM.config
    log: logs/dram/download_dram.log (check log file(s) for error details)
    conda-env: [...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_
    shell:
         DRAM-setup.py prepare_databases  --output_dir [...]dat/db/atlas/DRAM/db  --threads 8  --verbose  --skip_uniref  &> logs/dram/download_dram.log  ;  DRAM-setup.py export_config --output_file [...]dat/db/atlas/DRAM/DRAM.config
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Here is the relevant log output:

Traceback (most recent call last):                                                                                                                                                                                                                                               
  File "[...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_/bin/DRAM-setup.py", line 5, in <module>
    from mag_annotator.database_processing import (prepare_databases, update_dram_forms,
  File "[...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 13, in <module>
    from skbio import read as read_sequence
  File "[...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_/lib/python3.10/site-packages/skbio/__init__.py", line 11, in <module>
    import skbio.io  # noqa
  File "[...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_/lib/python3.10/site-packages/skbio/io/__init__.py", line 247, in <module>
    import_module('skbio.io.format.lsmat')
  File "[...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "[...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_/lib/python3.10/site-packages/skbio/io/format/lsmat.py", line 77, in <module>
    from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
  File "[...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_/lib/python3.10/site-packages/skbio/stats/distance/__init__.py", line 197, in <module>
    from ._mantel import mantel, pwmantel
  File "[...]dat/db/atlas/conda_envs/912ad4abbd015a117d8bf7520e1ca315_/lib/python3.10/site-packages/skbio/stats/distance/_mantel.py", line 16, in <module>
    from scipy.stats import PearsonRConstantInputWarning
ImportError: cannot import name 'PearsonRConstantInputWarning' from 'scipy.stats' (/zfshome/sukem066/.local/lib/python3.10/site-packages/scipy/stats/__init__.py)

Atlas version 2.16.3

• related to #562 but error still exists in latest atlas version
• maybe a special version of scikit-bio is needed? https://stackoverflow.com/questions/72744811/error-cannot-import-name-spearmanrconstantinputwarning-from-scipy-stats