diff --git a/pyani/scripts/subcommands/subcmd_aniblastall.py b/pyani/scripts/subcommands/subcmd_aniblastall.py
index 4dedc73..f91208c 100644
--- a/pyani/scripts/subcommands/subcmd_aniblastall.py
+++ b/pyani/scripts/subcommands/subcmd_aniblastall.py
@@ -43,7 +43,7 @@ from argparse import Namespace
 from logging import Logger
 
 
-def subcmd_aniblastall(args: Namespace, logger: Logger):
+def subcmd_aniblastall(args: Namespace):
     """Perform ANIblastall on all genome files in an input directory.
 
     :param args:
diff --git a/pyani/scripts/subcommands/subcmd_index.py b/pyani/scripts/subcommands/subcmd_index.py
index 8d7560c..30c896b 100644
--- a/pyani/scripts/subcommands/subcmd_index.py
+++ b/pyani/scripts/subcommands/subcmd_index.py
@@ -39,15 +39,16 @@
 # THE SOFTWARE.
 """Provides the index subcommand for pyani."""
 
+import logging
+
 from argparse import Namespace
-from logging import Logger
 
 from Bio import SeqIO
 
 from pyani import download, pyani_files
 
 
-def subcmd_index(args: Namespace, logger: Logger) -> int:
+def subcmd_index(args: Namespace) -> int:
     """Generate a file with the MD5 hash for each genome in an input directory.
 
     :param args:  Namespace, received command-line arguments
@@ -58,6 +59,8 @@ def subcmd_index(args: Namespace, logger: Logger) -> int:
 
     Genome files (FASTA) are identified from the file extension.
     """
+    logger = logging.getLogger(__name__)
+
     # Get list of FASTA files in the input directory
     logger.info("Scanning directory %s for FASTA files", args.indir)
     fpaths = pyani_files.get_fasta_paths(args.indir)

TypeError: subcmd_index() missing 1 required positional argument: 'logger'
#### Summary:
I am trying to index my local fasta format genomes and it gives the error that 1 positional argument 'logger' is missing


#### Description:
I am doing pyANI analysis, I downloaded the script from github and its dependencies. While indexing my fasta files for subsequent scirpts. It give a postional error in the script.
**Script**
pyani index indir ../../genomes/

#### Reproducible Steps:
Downloading any fasta format file from NCBI
Establishing pyANI (pyani version: 0.3.0-alpha) and its dependencies
running the script as mentioned with the indir argument.
pyani index indir ../../genomes/

#### Current Output:
TypeError: subcmd_index() missing 1 required positional argument: 'logger'

#### Expected Output:
md5 index files from fasta


#### pyani Version:
(pyani version: 0.3.0-alpha)

#### installed dependencies
bioconda 

#### Python Version:
Python 3.8
#### Operating System:

diff --git a/tests/test_subcmd_02_index.py b/tests/test_subcmd_02_index.py
index 6486785..400c186 100644
--- a/tests/test_subcmd_02_index.py
+++ b/tests/test_subcmd_02_index.py
@@ -83,7 +83,7 @@ class TestIndexSubcommand(unittest.TestCase):
         """Test indexing of downloaded files."""
         # Create index
         print(self.argsdict["index"])
-        subcommands.subcmd_index(self.argsdict["index"], self.logger)
+        subcommands.subcmd_index(self.argsdict["index"])
 
         # Check class and label files
         for fname in ("labels.txt", "classes.txt"):

pip install -e .[dev]
parse_log_pytest
requirements.txt
pytest pytest-cov
apt-get update apt-get install -y gcc
3.7
requirements.txt
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
biopython==1.81
certifi @ file:///croot/certifi_1671487769961/work/certifi
coverage==7.2.7
cycler==0.11.0
et-xmlfile==1.1.0
exceptiongroup==1.2.2
fonttools==4.38.0
importlib-metadata==6.7.0
iniconfig==2.0.0
kiwisolver==1.4.5
matplotlib==3.5.3
namedlist==1.8
networkx==2.6.3
numpy==1.21.6
openpyxl==3.1.3
packaging==24.0
pandas==1.3.5
Pillow==9.5.0
pluggy==1.2.0
-e git+https://github.com/widdowquinn/pyani.git@d67ce0d6b3b6137ad1d0955e12ba9db07fd6e835#egg=pyani
pyparsing==3.1.4
pytest==7.4.4
pytest-cov==4.1.0
python-dateutil==2.9.0.post0
pytz==2025.2
scipy==1.7.3
seaborn==0.12.2
six==1.17.0
SQLAlchemy==1.3.10
tomli==2.0.1
tqdm==4.67.1
typing_extensions==4.7.1
zipp==3.15.0

name: pyani
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - ca-certificates=2025.2.25=h06a4308_0
  - certifi=2022.12.7=py37h06a4308_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.4.4=h6a678d5_1
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - ncurses=6.4=h6a678d5_0
  - openssl=1.1.1w=h7f8727e_0
  - pip=22.3.1=py37h06a4308_0
  - python=3.7.16=h7a1cb2a_0
  - readline=8.2=h5eee18b_0
  - setuptools=65.6.3=py37h06a4308_0
  - sqlite=3.45.3=h5eee18b_0
  - tk=8.6.14=h39e8969_0
  - wheel=0.38.4=py37h06a4308_0
  - xz=5.6.4=h5eee18b_1
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - biopython==1.81
      - coverage==7.2.7
      - cycler==0.11.0
      - et-xmlfile==1.1.0
      - exceptiongroup==1.2.2
      - fonttools==4.38.0
      - importlib-metadata==6.7.0
      - iniconfig==2.0.0
      - kiwisolver==1.4.5
      - matplotlib==3.5.3
      - namedlist==1.8
      - networkx==2.6.3
      - numpy==1.21.6
      - openpyxl==3.1.3
      - packaging==24.0
      - pandas==1.3.5
      - pillow==9.5.0
      - pluggy==1.2.0
      - pyparsing==3.1.4
      - pytest==7.4.4
      - pytest-cov==4.1.0
      - python-dateutil==2.9.0.post0
      - pytz==2025.2
      - scipy==1.7.3
      - seaborn==0.12.2
      - six==1.17.0
      - sqlalchemy==1.3.10
      - tomli==2.0.1
      - tqdm==4.67.1
      - typing-extensions==4.7.1
      - zipp==3.15.0
prefix: /opt/conda/envs/pyani

tests/test_subcmd_02_index.py::TestIndexSubcommand::test_index
pyani/scripts/subcommands/subcmd_aniblastall.py pyani/scripts/subcommands/subcmd_index.py
pyani/scripts/subcommands/subcmd_aniblastall.py pyani/scripts/subcommands/subcmd_index.py