2026-05-16 21:20:40,491 - INFO - ================================================================================
2026-05-16 21:20:40,491 - INFO - ASSAY CALIBRATION PIPELINE
2026-05-16 21:20:40,491 - INFO - ================================================================================
2026-05-16 21:20:40,491 - INFO - 
Dataset: MSH2_Jia_2021
2026-05-16 21:20:40,491 - INFO - Input: example/MSH2_Jia_2021.csv
2026-05-16 21:20:40,491 - INFO - Output: /var/www/html/ExCALIBR/tests/fixtures
2026-05-16 21:20:40,491 - INFO - Components: [2]
2026-05-16 21:20:40,491 - INFO - Bootstraps: 50
2026-05-16 21:20:40,491 - INFO - Execution: parallel
2026-05-16 21:20:40,491 - INFO - 
================================================================================
2026-05-16 21:20:40,491 - INFO - STEP 1: Bootstrap Fitting
2026-05-16 21:20:40,491 - INFO - ================================================================================
2026-05-16 21:23:50,512 - INFO - 
Completed 50 bootstrap iterations
2026-05-16 21:23:50,513 - INFO - 
Using fitted components: ['2c']
2026-05-16 21:23:50,513 - INFO - 
================================================================================
2026-05-16 21:23:50,513 - INFO - STEP 3: Visualization and Export
2026-05-16 21:23:50,513 - INFO - ================================================================================
2026-05-16 21:23:54,145 - INFO - 
Processing 2c...
2026-05-16 21:23:54,145 - INFO -   Valid fits: 50/50
2026-05-16 21:23:54,145 - WARNING -   No synonymous sample, setting benign_method from avg to benign
2026-05-16 21:23:54,145 - INFO -   Sample indices: P=0, B=1, G=2, S=None
2026-05-16 21:24:38,049 - INFO -   Valid priors: 47
2026-05-16 21:24:38,050 - INFO -   Prior: 0.014191
2026-05-16 21:24:47,908 - INFO -   Scoreset flipped: True
2026-05-16 21:24:47,909 - INFO -   Using median prior for unified thresholds
2026-05-16 21:24:52,338 - INFO -   Final point ranges computed: 6 non-empty
2026-05-16 21:24:53,123 - INFO -   Saved visualization: /var/www/html/ExCALIBR/tests/fixtures/MSH2_Jia_2021_2c_visualization.png
2026-05-16 21:24:53,296 - INFO - 
================================================================================
2026-05-16 21:24:53,296 - INFO - STEP 3b: Per-Variant Evidence Table
2026-05-16 21:24:53,296 - INFO - ================================================================================
2026-05-16 21:24:56,760 - INFO -   Standard evidence assigned to 1579 variants
2026-05-16 21:24:56,766 - INFO -   Saved variant table: /var/www/html/ExCALIBR/tests/fixtures/MSH2_Jia_2021_2c_variants.csv (1579 variants)
2026-05-16 21:24:56,766 - INFO - 
================================================================================
2026-05-16 21:24:56,766 - INFO - STEP 4: Saving Results
2026-05-16 21:24:56,766 - INFO - ================================================================================
2026-05-16 21:24:56,767 - INFO -   Saved calibration: /var/www/html/ExCALIBR/tests/fixtures/MSH2_Jia_2021_2c_calibration.json
2026-05-16 21:24:56,773 - INFO -   Saved bootstrap fits: /var/www/html/ExCALIBR/tests/fixtures/MSH2_Jia_2021_bootstrap_fits.json.gz (0.0 MB)
2026-05-16 21:24:56,773 - INFO - 
================================================================================
2026-05-16 21:24:56,773 - INFO - PIPELINE COMPLETE
2026-05-16 21:24:56,773 - INFO - ================================================================================
2026-05-16 21:24:56,773 - INFO - 
Results saved to: /var/www/html/ExCALIBR/tests/fixtures
2026-05-16 21:24:56,773 - INFO -   - Calibration: MSH2_Jia_2021_<component>_calibration.json
2026-05-16 21:24:56,773 - INFO -   - LR values: MSH2_Jia_2021_<component>_lr_values.json.gz
2026-05-16 21:24:56,773 - INFO -   - Visualization: MSH2_Jia_2021_<component>_visualization.png
2026-05-16 21:24:56,773 - INFO -   - Variant table: MSH2_Jia_2021_<component>_variants.csv
2026-05-16 21:24:56,773 - INFO -   - Bootstrap fits: MSH2_Jia_2021_bootstrap_fits.json.gz