[Bug]: TypeError: 'NoneType' object is not subscriptable

[hjbsmith]

Checklist

• Find the offending file in the output. If processing halts, re-run analysis with topostats --core 1 process.
• Describe the bug.
• Include the configuration file.
• Copy of the log-file from running with topostats --log-level debug <command>.
• The exact command that failed. This is what you typed at the command line, including any options.
• TopoStats version, this is reported by topostats --version
• Operating System and Python Version

Describe the bug

Topostats only partially runs and generates half of the output. I have attached the output message I received

Copy of the log-file from running with topostats --log-level debug <command>

20251009_YS_ApHU_nativeSC_APS_NaCl-2025-10-15-10-08-42.log

Include the configuration file

config.yaml

To Reproduce

Command used: topostats --config config.yaml process

File that caused the error, can be accessed through this link:
https://drive.google.com/drive/folders/1AiXfxUZDQjQ-1_mlSxrWAAgtuTzKIXUE?usp=share_link

TopoStats Version

Git main branch

Python Version

3.11

Operating System

MacOS M1/M2 (post-2021)

Python Packages

Topostats 2.3.1