AlphaFold2_mmseqs2 crashed upon processing protein sequence with repeat

Hi,

I tried running AlphaFold2_mmseqs2 on these two files separately:

>HHAWx4
HHAWHHAWHHAWHHAW

And

>KKAWx4
KKAWKKAWKKAWKKAW

Although the sequences are valid amino acids, it gave me the following error message:

running mmseqs2
  0%|          | 0/150 [elapsed: 00:00 remaining: ?]
Traceback (most recent call last):
  File "/home/ubuntu/storage1/colabfold/runner_af2advanced.py", line 163, in <module>
    hhfilter_loc="colabfold-conda/bin/hhfilter", precomputed=precomputed, TMP_DIR=output_dir)
  File "/home/ubuntu/storage1/colabfold/colabfold_alphafold.py", line 292, in prep_msa
    A3M_LINES = cf.run_mmseqs2(I["seqs"], prefix, use_filter=True, host_url=mmseqs_host_url)
  File "/home/ubuntu/storage1/colabfold/colabfold.py", line 150, in run_mmseqs2
    raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.')
Exception: MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.

How can I resolve the issue?

G.V.

Start with runner_af2advanced.py and trace prep_msa in colabfold_alphafold.py into run_mmseqs2 in colabfold.py. Reproduce the failure using the two sequences from the report and inspect how the MMseqS2 API response is handled. Done means determining whether the repeated valid sequences expose a project bug or an external API failure and documenting or fixing the identified behavior.