Should mmseq2 be skipped, when --use-templates and --custom-template-path and custom MSA are provided?

Expected Behavior

Skip mmseq2 search.

Current Behavior

In code around line 1364 in colabfold/batch.py, it seems even when use_templates is True, a3m_lines is not None (use custom MSA) and custom_template_path is specified (not None), the first if statement is True and mmseq2 is called. Should not mmseq2 be skipped inside the get_msa_and_templates method?

Thanks.

        ###########################################
        # generate MSA (a3m_lines) and templates
        ###########################################
        try:
            if use_templates or a3m_lines is None:
                (unpaired_msa, paired_msa, query_seqs_unique, query_seqs_cardinality, template_features) \
                = get_msa_and_templates(jobname, query_sequence, result_dir, msa_mode, use_templates, 
                    custom_template_path, pair_mode, host_url)
            if a3m_lines is not None:
                (unpaired_msa, paired_msa, query_seqs_unique, query_seqs_cardinality, template_features_) \
                = unserialize_msa(a3m_lines, query_sequence)
                if not use_templates: template_features = template_features_

Steps to Reproduce (for bugs)

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ColabFold Output (for bugs)

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Context

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Your Environment

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Start in colabfold/batch.py around line 1364 and trace get_msa_and_templates alongside the custom-MSA path. Check the combination of use_templates=True, provided a3m_lines, and custom_template_path; done means mmseq2 is skipped for that combination while other behavior remains unchanged.