MMseqs2 result2msa step fails due to incorrect database type

[real-junjiezhang]

I am using the following MMseqs2 pipeline to process my dataset:

1. mmseqs createdb query.fasta qdb
2. mmseqs search qdb target result tmp
3. mmseqs result2msa qdb target result result_msa
4. mmseqs unpackdb result_msa outdir

My goal is to generate 1000 corresponding A3M files for the 1000 sequences in my query FASTA file. However, I encountered an issue in step 3 (result2msa).

Issue Description

After running mmseqs search, instead of generating a single result database, MMseqs2 produces multiple files (result.0, result.1, result.2, ...). When I attempt to run mmseqs result2msa, I get the following error:

Input database "/path/result.0" has the wrong type (Generic)
Allowed input:

• Alignment
• Prefilter
• Bi-directional prefilter
• Clustering

It seems that theresult.0database format is not as expected. How can I correctly generate the required alignment database so that result2msa runs successfully?

Any guidance on resolving this issue would be greatly appreciated!