Predictive proteins folder empty

[zinfin]

@Noonanav when running the protein-family-worfklow with a phenotype matrix with more than two columns with the regression task type, the modeling_results/model_performance/predictive_proteins folder is empty. In my case I had a phenotype matrix with the following columns:

Here's the command that was used:

genophi protein-family-workflow --input_path_strain /data/od_strains --phenotype_matrix /data/GenoPHI/data/interation_matrices/260212_clean_relative_ods.csv --output ec_m9_no_outliers_v2/ --threads 24 --sample_column strain --phenotype_column relative_od --task_type regression --max_ram 24 --method rfe --num_runs_fs 25 --num_runs_modeling 50 --use_shap

And output from the log:

2026-03-05 01:35:49,903 - INFO - Step 5: Selecting top-performing cutoff and running predictive proteins workflow...
2026-03-05 01:35:49,904 - INFO - Step 1: Extracting predictive features.
2026-03-05 01:35:49,908 - INFO - Predictive feature groups detected: ['Inoculation_datec', 'sc', 'undiluted_ODc']
2026-03-05 01:35:49,908 - WARNING - More than two feature groups detected. Please ensure the correct feature groups are selected.
2026-03-05 01:35:49,908 - ERROR - An error occurred: local variable 'strain_features' referenced before assignment
2026-03-05 01:35:49,908 - INFO - Report saved to: ec_m9_no_outliers_v2/workflow_report.txt
2026-03-05 01:35:49,909 - INFO - CSV log saved to ec_m9_no_outliers_v2/workflow_report.csv.
2026-03-05 01:35:49,909 - ERROR - An error occurred: local variable 'strain_features' referenced before assignment
Traceback (most recent call last):
  File "/data/GenoPHI/genophi/cli.py", line 1402, in main
    protein_family_workflow_command(args)
  File "/data/GenoPHI/genophi/cli.py", line 1290, in protein_family_workflow_command    
    run_protein_family_workflow(
  File "/data/GenoPHI/genophi/workflows/protein_family_workflow.py", line 435, in run_protein_family_workflow
    run_predictive_proteins_workflow( 
  File "/data/GenoPHI/genophi/workflows/feature_annotations_workflow.py", line 60, in run_predictive_proteins_workflow
    select_features = get_predictive_features(feature_file_path, feature_type=feature_type, sample_column=strain_column, phenotype_column=phenotype_column)
  File "/data/GenoPHI/genophi/feature_annotations.py", line 102, in get_predictive_features
    predictive_features = strain_features
UnboundLocalError: local variable 'strain_features' referenced before assignment