haydenji0731
commented
1 day ago I would try removing the gffutils DB that was previously created by LiftOff and then re-run the tool. The error indicates that the features DB wasn't successfully constructed.
If your problem persists, I can try looking at your reference annotation.
Traceback (most recent call last):t-order relations: 2374000 features
File "/home1/06127/pdoris/miniforge3/envs/liftoff/bin/liftoff", line 10, in
sys.exit(main())
File "/home1/06127/pdoris/miniforge3/envs/liftoff/lib/python3.8/site-packages/liftoff/run_liftoff.py", line 12, in main
run_all_liftoff_steps(args)
File "/home1/06127/pdoris/miniforge3/envs/liftoff/lib/python3.8/site-packages/liftoff/run_liftoff.py", line 24, in run_all_liftoff_steps
feature_db, feature_hierarchy, ref_parent_order = liftover_types.lift_original_annotation(ref_chroms, target_chroms,
File "/home1/06127/pdoris/miniforge3/envs/liftoff/lib/python3.8/site-packages/liftoff/liftover_types.py", line 11, in lift_original_annotation
feature_hierarchy, feature_db, ref_parent_order = extract_features.extract_features_to_lift(ref_chroms,
File "/home1/06127/pdoris/miniforge3/envs/liftoff/lib/python3.8/site-packages/liftoff/extract_features.py", line 17, in extract_features_to_lift
feature_db = create_feature_db_connections(args)
File "/home1/06127/pdoris/miniforge3/envs/liftoff/lib/python3.8/site-packages/liftoff/extract_features.py", line 33, in create_feature_db_connections feature_db = build_database(args.db, args.g, disable_transcripts, disable_genes) File "/home1/06127/pdoris/miniforge3/envs/liftoff/lib/python3.8/site-packages/liftoff/extract_features.py", line 48, in build_database return feature_db UnboundLocalError: local variable 'feature_db' referenced before assignment