use MSA and custom template simultaneously?

Expected Behavior

I would like to use both MSA and custom templates (one or more) simultaneously.

Current Behavior

I can get MSA or custom templates method to work, but not both.

Steps to Reproduce (for bugs)

colabfold_batch is newest version built on a local workstation running Ubuntu 20.04.

colabfold_batch --amber --templates --num-recycle 5 --use-gpu-relax --msa-mode "MMseqs2 (UniRef+Environmental)" --custom-template-path template/ sequence.csv output/

ColabFold Output (for bugs)

2022-11-02 11:09:15,687 Running colabfold 1.3.0 (979009c4740b398fa817f9e2c8dae2ff832575df)
2022-11-02 11:09:16,288 --max-msa can not be used in combination with AlphaFold2-multimer (--max-msa ignored)
2022-11-02 11:09:18,341 Found 8 citations for tools or databases
2022-11-02 11:09:20,878 Query 1/1: ************************** (length 1288)
2022-11-02 11:09:28,977 Sequence 0 found templates: ['9yzy_B', '9yzy_A', '9yzy_A', '9yzy_B', '9yzy_A', '9yzy_B', '9yzy_A', '9yzy_B']
2022-11-02 11:09:29,773 Running model_3

It seems only a custom template was used, but no MSA was queried.

Context

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Operating system and version: Ubuntu 20.04.

Start at the colabfold_batch entry point and reproduce the reported command with --templates, --custom-template-path, and the selected --msa-mode. Trace why the output says that no MSA was queried despite finding templates. Done means one run uses both the MSA and custom templates, with output confirming both.