submatrix command creates empty dists output when run on valid clustering output directory

[the-alquemist]

Description

The submatrix command appears to complete without errors, but generates an empty output. Specifically, the resulting submatrix/dists directory is empty and the generated log file contains little or no useful diagnostic information.

Clustering itself completes successfully, and all expected output files are present beforehand.

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Environment

• Pling version: 3.0.1
• Installation method: conda
• OS: Fedora 43

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Workflow

1. Run clustering

pling cluster align <absolute_path/input_1> <absolute_path/output_1> --cores 14 --visualisation all --output_type both

Clustering completes successfully and produces expected outputs.

The output directory contains:

• containment files
• distance matrices
• typing files
• visualization outputs

Visualizations can also be served successfully via:

python -m http.server 8000 --bind 127.0.0.1

2. Run submatrix

pling submatrix <absolute_path/output_1> --cores 14

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Observed Behavior

A submatrix directory is created inside the original clustering output directory, but:

• submatrix/dists/ is empty
• the generated log file contains almost no information
• log reports the job as a successful operation
• no explicit error message is shown

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Expected Behavior

Expected the submatrix command to generate distance submatrices from the existing clustering output directory.