Two MSA results in --msa-only output

[NooraAz]

Expected Behavior

I'm using --msa-only mode to get the MSA file and it runs without issues. However, in the generated *.a3m file, I notice that there are two lines for >101, and it is like there are two different MSA results appended together. For example, when I plot query coverage ordered by lines in the file, the coverage goes down, and then it peaks. (This is the place for the second >101 header).

Current Behavior

x = line number y = query coverage

The .a3m file is attached as .txt (github doesn't allow loading a3m) CUTINASE.txt

This is the Fasta file used as input (in .txt format) 1CUS.txt

Command used

colabfold_batch --msa-only 1CUS.fasta <output-directory>