Local MSA results different from MSA server

Expected Behavior

I expect using colabfold_search with locally prepared DBs to give the same MSA results as those using colabfold_batch with the MSA server.

Current Behavior

The two give different MSA results given the same input .fasta.

Steps to Reproduce (for bugs)

1. Install colabfold==1.5.5 via pip to a fresh new mamba environment (python==3.11.10).

2. Build mmseqs2 of commit 71dd32ec43e3ac4dabf111bbc4b124f1c66a85f1 following ColabFold README.

3. Execute the following to set up the DBs:

   MMSEQS_NO_INDEX=1 bash setup_databases.sh $colabfold_db_dir
   

   where I use the mmseqs2 built from step 2 for the tsv2exprofiledb commands.

4. Prepare a sample .fasta file (say sample.fasta) of a single protein sequence.

5. Get a locally generated MSA by:

   colabfold_search --mmseqs $mmseqs sample.fasta $colabfold_db_dir out_local
   # $mmseqs == mmseqs2 executable from step 2
   # Adding args `--db2 pdb100_230517` gave no change in the MSA outputs.
   

6. Independently, get a MSA generated by querying the server like:

   colabfold_batch sample.fasta out_server --msa-only
   

7. Compare the .a3m files generated from steps 5 and 6.

ColabFold Output (for bugs)

Omitted; I can attach outputs if necessary.

Context

I want to reproduce results from ColabFold notebooks on my local machine.

Your Environment

• Git commit used: e2ca9e8f992cd65c986de5b64885d5572d8b8ad9
  where I used the ColabFold code only for executing setup_databases.sh. For colabfold_{search,batch} commands, I used v1.5.5 installed via pip.
• Operating system and version: Red Hat Enterprise Linux 9.3 (Plow)

Start by reproducing the comparison with colabfold_search and colabfold_batch using the sample.fasta and locally prepared databases from setup_databases.sh. Compare the generated .a3m files while checking the reported ColabFold and mmseqs2 versions; the issue is done when equivalent local and server runs produce matching MSA results or the discrepancy is explained.