Local generation of .m8 file causes wrong template selection in colabfold_batch

Expected Behavior

This is my input.csv file:

id,sequence
heterodimer_2,MAAEAWRSRFRERVVEAAERWESVGESLATALTHLKSPMHAGDEEEAAAARTRIQLAMGELVDASRNLASAMSLMKVAELLALHGGSVNPSTHLGEISLLGDQYLAERNAGIKLLEAGKDARKAYISVDGCRGNLDAILLLLDHPRVPCVDDFIEEELFVAGDNLQGAIGNAKLGTERAVGARQDVSGAN:MDAAVAGQHARRRIRPPEPLVMAGSPSTPAAFRCPISLEVMRSPVSLPTGATYDRASIQRWLDTGHRTCPATRLPLASTDLVPNLLLRRLIHLHAATLPPSPSPEVVLSQLAAAGGEPAAAEKAVRSLAAKIAPEKGKRASVASAVAADLDSAVPALLSFAKGGAGADARVDAVRILATVAPELVPYLTGDGTEKRGRVRMAVEALAAVLSADGVGEDTKEGLIAALVAGDLGHIVNTLIAAGANGVMVLETILTSPVPDADAKTAIADRSELFPDLVRILKDAASPAAIRCMAAAVQVRGRPARSSMVRAGAIPALALAVAAAPTAVAESALGLLVEAARCTDGKAAIGADAAEVAAAVMGRMIRVGPAGREFAVAVLWLSCCAGGGDRRMREAVASAPEAVGKLLVVMQGDCSPSTSRMAGELLRAVRMEQERKGLAAAYDSRTIHVMPY

Running colabfold_batch --templates --amber --use-gpu-relax input.csv output yields the following .m8 file and template_domain_names.json file:
First 10 lines of .m8:

101     7x8v_E  1.000   184     0       0       4       187     1       184     1.956E-67       228     184M
102     7c96_B  0.528   70      33      0       26      95      1       70      6.214E-22       103     70M
102     1t1h_A  0.520   75      36      0       24      98      1       75      1.968E-20       98      75M
102     1t1h_A  0.520   75      36      0       24      98      1       75      1.968E-20       98      75M
102     1t1h_A  0.520   75      36      0       24      98      1       75      1.968E-20       98      75M
102     1t1h_A  0.520   75      36      0       24      98      1       75      1.968E-20       98      75M
102     2f42_A  0.347   72      47      0       27      98      63      134     5.527E-15       81      72M
102     2oxq_D  0.333   72      48      0       27      98      1       72      1.714E-14       79      72M
102     2c2v_U  0.367   68      43      0       27      94      1       68      1.714E-14       79      68M
102     2c2v_S  0.367   68      43      0       27      94      1       68      1.714E-14       79      68M

template_domain_names.json:
{"A": ["7x8v_E", "7x8v_E"], "B": ["7c96_B", "2c2l_C", "2c2l_D", "1t1h_A", "2f42_A", "2oxq_D", "2c2v_T", "2c2v_U", "2c2v_S", "2c2v_V", "7bbd_B", "6fga_E", "5olm_B", "8a58_D", "6fga_H", "6fga_D", "6s53_H"]}

This is to be expected I guess.

Current Behavior

When running everything locally like this:

input_file="input.csv"
DATABASE_PATH="/data/gpfs/datasets/mmseqs/uniref30_2302"

colabfold_search \
  --use-env 1 \
  --use-templates 1 \
  --db-load-mode 2 \
  --mmseqs /apps/easybuild-2022/easybuild/software/MPI/GCC/11.3.0/OpenMPI/4.1.4/MMseqs2/15-6f452/bin/mmseqs \
  --db2 pdb100_230517 \
  --threads 8 \
  ${input_file} \
  ${DATABASE_PATH} \
  msas

LOCALPDBPATH="/data/scratch/datasets/alphafold/v2.3.2/pdb_mmcif/mmcif_files"
RANDOMSEED=0
PDBHITFILE="heterodimer_2_pdb100_230517.m8"

  # Run the colabfold_batch command
  colabfold_batch \
    --amber \
    --templates \
    --use-gpu-relax \
    --pdb-hit-file msas/${PDBHITFILE} \
    --local-pdb-path ${LOCALPDBPATH} \
    --random-seed ${RANDOMSEED} \
    msas/heterodimer_2.a3m \
    output

I get the same .m8 file as above, however, the template_domain_names.json file is different and contains templates for A that are not in the .m8 file:
{"A": ["7x8v_A", "7x8v_A", "7x8v_A", "7x8v_A", "7x8v_A", "7x8v_A", "6s53_I", "6s53_K", "7bbd_D"], "B": ["1t1h_A", "2f42_A", "7c96_B", "2c2l_C", "2c2l_B", "2c2l_A", "2c2l_D", "2c2v_S", "2c2v_T", "2oxq_D", "2c2v_U", "2oxq_C", "2c2v_V", "5olm_B", "7bbd_B", "6s53_G", "6s53_A", "6fga_C", "6fga_F", "6fga_H"]}

##Output

2024-02-29 10:41:22,688 Running colabfold 1.5.5 (06c775a287a891b5f8e81a88e52bcadc4dd67cd2)
2024-02-29 10:44:15,727 Running on GPU
2024-02-29 10:44:16,392 Found 9 citations for tools or databases
2024-02-29 10:44:19,723 WARNING: Found 20 models in predictions_56426093/templates/1t1h.cif. The first model will be used as a template.
2024-02-29 10:44:21,434 Query 1/1: heterodimer_2 (length 642)
2024-02-29 10:44:29,529 Sequence 0 found templates: ['7x8v_A', '7x8v_A', '7x8v_A', '7x8v_A', '7x8v_A', '7x8v_A', '6s53_I', '6s53_K', '7bbd_D']
2024-02-29 10:44:33,588 Sequence 1 found templates: ['1t1h_A', '2f42_A', '7c96_B', '2c2l_C', '2c2l_B', '2c2l_A', '2c2l_D', '2c2v_S', '2c2v_T', '2oxq_D', '2c2v_U', '2oxq_C', '2c2v_V', '5olm_B', '7bbd_B', '6s53_G', '6s53_A', '6fga_C', '6fga_F', '6fga_H']
2024-02-29 10:44:35,289 Setting max_seq=508, max_extra_seq=1690
2024-02-29 10:47:22,893 alphafold2_multimer_v3_model_1_seed_000 recycle=0 pLDDT=76.4 pTM=0.519 ipTM=0.142
2024-02-29 10:47:33,100 alphafold2_multimer_v3_model_1_seed_000 recycle=1 pLDDT=83.8 pTM=0.744 ipTM=0.823 tol=10.6
2024-02-29 10:47:43,307 alphafold2_multimer_v3_model_1_seed_000 recycle=2 pLDDT=85.1 pTM=0.759 ipTM=0.866 tol=4.78
2024-02-29 10:47:53,510 alphafold2_multimer_v3_model_1_seed_000 recycle=3 pLDDT=85.2 pTM=0.754 ipTM=0.857 tol=2.23
2024-02-29 10:48:03,729 alphafold2_multimer_v3_model_1_seed_000 recycle=4 pLDDT=85.6 pTM=0.762 ipTM=0.869 tol=0.629
2024-02-29 10:48:13,948 alphafold2_multimer_v3_model_1_seed_000 recycle=5 pLDDT=85.5 pTM=0.758 ipTM=0.867 tol=0.294

Question

The templates 6s53_I, 6s53_K and 7bbd_D should not be used for protein A, based on the .m8 file.
I have not been able to fully understand how the template_domain_names.json is generated within the code.
In general the template generation does not seem to be consistent. Is this something that can be solved? Is there something wrong in my approach?

Start at the colabfold_search and colabfold_batch entry points, tracing how the .m8 file and template_domain_names.json are produced from input.csv and the supplied PDB hit file. Compare the templates selected for protein A with the .m8 records; the work is done when the generated JSON is consistent with those records.