Crash during "ANALYZE features", reported as: KeyError: ''

[J-Calvelo]

Hello. I just ran into this issue. Not sure what could be the cause

2024-11-26 13:26:38,610 - INFO - Populating features
2024-11-26 13:29:46,570 - INFO - Populating features table and first-order relations: 1421934 features
2024-11-26 13:29:46,570 - INFO - Updating relations
2024-11-26 13:30:08,876 - INFO - Creating relations(parent) index
2024-11-26 13:30:10,282 - INFO - Creating relations(child) index
2024-11-26 13:30:12,118 - INFO - Creating features(featuretype) index
2024-11-26 13:30:13,081 - INFO - Creating features (seqid, start, end) index
2024-11-26 13:30:14,354 - INFO - Creating features (seqid, start, end, strand) index
2024-11-26 13:30:15,682 - INFO - Running ANALYZE features
2024-11-26 13:30:19,861 - INFO - Populating features
2024-11-26 13:32:55,597 - INFO - Populating features table and first-order relations: 1165093 features
2024-11-26 13:32:55,598 - INFO - Updating relations
2024-11-26 13:33:14,079 - INFO - Creating relations(parent) index
2024-11-26 13:33:15,235 - INFO - Creating relations(child) index
2024-11-26 13:33:16,737 - INFO - Creating features(featuretype) index
2024-11-26 13:33:17,470 - INFO - Creating features (seqid, start, end) index
2024-11-26 13:33:18,588 - INFO - Creating features (seqid, start, end, strand) index
2024-11-26 13:33:19,762 - INFO - Running ANALYZE features
Traceback (most recent call last):
  File "/fs1/local/cqls/software/x86_64/liftofftools-0.4.4/.pixi/envs/default/bin/liftofftools", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/fs1/local/cqls/software/x86_64/liftofftools-0.4.4/.pixi/envs/default/lib/python3.12/site-packages/liftofftools/liftofftools.py", line 34, in main
    analyze_clusters.main(ref_proteins, target_proteins, ref_trans, target_trans, ref_db, target_db, args)
  File "/fs1/local/cqls/software/x86_64/liftofftools-0.4.4/.pixi/envs/default/lib/python3.12/site-packages/liftofftools/cluster_analysis/analyze_clusters.py", line 14, in main
    run_coding_workflow(ref_proteins, ref_db, target_db, target_proteins,ref_trans, target_trans, args)
  File "/fs1/local/cqls/software/x86_64/liftofftools-0.4.4/.pixi/envs/default/lib/python3.12/site-packages/liftofftools/cluster_analysis/analyze_clusters.py", line 21, in run_coding_workflow
    unmapped_coding = analyze_proteins(ref_proteins, ref_db, target_db, target_proteins, args)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/fs1/local/cqls/software/x86_64/liftofftools-0.4.4/.pixi/envs/default/lib/python3.12/site-packages/liftofftools/cluster_analysis/analyze_clusters.py", line 37, in analyze_proteins
    ref_clusters, target_clusters = cluster(ref_proteins, target_proteins, ref_protein_coding_genes,
                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/fs1/local/cqls/software/x86_64/liftofftools-0.4.4/.pixi/envs/default/lib/python3.12/site-packages/liftofftools/cluster_analysis/analyze_clusters.py", line 48, in cluster
    target_tsv = build_clusters(target_seqs,  target_genes, target_output, args)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/fs1/local/cqls/software/x86_64/liftofftools-0.4.4/.pixi/envs/default/lib/python3.12/site-packages/liftofftools/cluster_analysis/analyze_clusters.py", line 107, in build_clusters
    longest_seqs = sequence_dict.get_longest_isoform_dict(gene_list)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/fs1/local/cqls/software/x86_64/liftofftools-0.4.4/.pixi/envs/default/lib/python3.12/site-packages/liftofftools/sequences.py", line 53, in get_longest_isoform_dict
    longest_isoform_dict[gene] = self[longest_isoform]
                                 ~~~~^^^^^^^^^^^^^^^^^
KeyError: ''

The command was:
liftofftools all -dir /nfs6/IB/Blouin_Lab/users/javierc/ANALYSIS/Key_Region_Anotation/Annotation_Transfer_Liftoff/Lifftoftools_checks/Bg_2024_transfered_to_Bg_2024_vs_1316_R_i36_B_liftofftools_out -edit-distance -r /nfs6/IB/Blouin_Lab/users/javierc/ANALYSIS/Key_Region_Anotation/Annotation_Transfer_Liftoff/Temp_Files/Sequences/Bg_2024_genome.fasta -t /nfs6/IB/Blouin_Lab/users/javierc/ANALYSIS/Key_Region_Anotation/Annotation_Transfer_Liftoff/Lifftoftools_checks/Simplified_Sequences/Bg_2024_transfered_to_Bg_2024_vs_1316_R_i36_B_short.fasta -rg /nfs6/IB/Blouin_Lab/users/javierc/ANALYSIS/Key_Region_Anotation/Annotation_Transfer_Liftoff/Temp_Files/Annotations/Round_1/Bg_2024_annotation.gff -tg /nfs6/IB/Blouin_Lab/users/javierc/ANALYSIS/Key_Region_Anotation/Annotation_Transfer_Liftoff/Lifftoftools_checks/Simplified_GFFs/Bg_2024_transfered_to_Bg_2024_vs_1316_R_i36_B_scaffolded_only.gff