chewBBACA version: 3.3.2
Authors: Rafael Mamede, Pedro Cerqueira, Mickael Silva, João Carriço, Mário Ramirez
Github: https://github.com/B-UMMI/chewBBACA
Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
Contacts: imm-bioinfo@medicina.ulisboa.pt

==================================
  chewBBACA - PrepExternalSchema
==================================
Started at: 2025-06-25T10:50:29

Number of cores: 2
BLAST Score Ratio: 0.6
Translation table: 11
Using a minimum length value of 0 for schema adaptation and 0 to store in the schema config file.
Using a size threshold value of None for schema adaptation and 0.2 to store in the schema config file.
Number of loci to adapt: 2513

Determining the total number of alleles and allele mean length per gene...

Adapting 2513 loci...

 [====                ] 23%
Error on adapt_loci:
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/site-packages/CHEWBBACA/utils/multiprocessing_operations.py", line 42, in function_helper
    results = input_args[-1](*input_args[0:-1])
  File "/usr/local/lib/python3.10/site-packages/CHEWBBACA/PrepExternalSchema/adapt_schema.py", line 312, in adapt_loci
    bsr_categorizer(blast_results, representatives,
  File "/usr/local/lib/python3.10/site-packages/CHEWBBACA/PrepExternalSchema/adapt_schema.py", line 84, in bsr_categorizer
    bsr_values = [float(res[-1])/float(representatives_scores[res[0]])
  File "/usr/local/lib/python3.10/site-packages/CHEWBBACA/PrepExternalSchema/adapt_schema.py", line 84, in <listcomp>
    bsr_values = [float(res[-1])/float(representatives_scores[res[0]])
KeyError: '219'


 [====================] 100%Traceback (most recent call last):
  File "/usr/local/bin/chewie", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/CHEWBBACA/chewBBACA.py", line 1654, in main
    functions_info[process][1]()
  File "/usr/local/lib/python3.10/site-packages/CHEWBBACA/utils/process_datetime.py", line 146, in wrapper
    func(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/CHEWBBACA/chewBBACA.py", line 1091, in run_adapt_schema
    adapt_schema.main(loci_list, output_dirs,
  File "/usr/local/lib/python3.10/site-packages/CHEWBBACA/PrepExternalSchema/adapt_schema.py", line 440, in main
    invalid_alleles = [f'{allele[0]}: {allele[1]}' for allele in invalid_alleles]
  File "/usr/local/lib/python3.10/site-packages/CHEWBBACA/PrepExternalSchema/adapt_schema.py", line 440, in <listcomp>
    invalid_alleles = [f'{allele[0]}: {allele[1]}' for allele in invalid_alleles]
IndexError: string index out of range
make: *** [Makefile:604: /home/katjast/GMS_jasen/jasen_250623/assets/cgmlst/escherichia_coli/alleles_rereffed] Error 1