Discrepancies in Template Search Between Server and Local With Same Input MSA

Expected Behavior

When running ColabFold locally, the template search should produce identical results to those generated by the server. Specifically, the templates returned from the local run should match those returned from the server, given that both use the same MSA and pdb70.m8 input files.

Current Behavior

There is a discrepancy in template search results. The server returns a different set of templates compared to the local run, despite using the same input MSA and pdb70.m8 files.

Steps to Reproduce

I obtained MSA and pdb70.m8 files from a server run.
Ran the local command:
colabfold_batch --templates --local-pdb-path /runtime/databases/mmseqs_2-colabfold/pdb/divided --pdb-hit-file ./server_generated_pdb70.m8 --num-seeds 5 --num-models 5 ./server_generated_msa.a3m ./output_folder

And got this:
2025-01-15 08:31:45,655 Sequence 0 found templates: ['8f7w_A', '8efb_A', '7xa3_A', '7x9y_A', '7vl8_A', '7vla_A', '7o7f_A', '6dde_A', '7sbf_A', '7u2l_A']
2025-01-15 08:31:54,201 Sequence 1 found templates: ['7vla_R', '7o7f_C', '7vl8_R', '6meo_B', '7x9y_R', '7f1q_R', '7xa3_R', '4n6h_A', '7t10_R', '7yit_A', '8ef5_M', '8ef5_R', '4rwa_B', '8efb_R', '4rwa_A', '8f7w_R', '7u2l_D', '7ul4_A', '6b73_A', '7sbf_R']

Compared to doing the template search on the server:
colabfold_batch --templates --num-seeds 5 --num-models 5 ./server_generated_msa.a3m ./output_folder

Which gives:
2025-01-14 06:42:50,723 Sequence 0 found no templates
2025-01-14 06:43:04,722 Sequence 1 found templates: ['7vla_R', '7vl8_R', '7o7f_C', '7xa3_R', '6meo_B', '7f1q_R', '7x9y_R', '4n6h_A', '4rwa_B', '8ef5_M', '8efb_R', '7t10_R', '7ul4_A', '7u2l_D', '7sbf_R', '6dde_R', '6vi4_A', '6b73_A', '8f7w_R', '7yit_A']

Given my input, I would expect the server’s results for the template search rather than the local ones.

Any help with understanding why this discrepancy is occurring will be much appreciated!
Thanks

Start by comparing the two shown colabfold_batch invocations and their server-generated_msa.a3m and server_generated_pdb70.m8 inputs. Trace the template-search entry point and compare the local and server template lists for both sequences; done means identifying why identical inputs produce different results or documenting the relevant environmental difference.