HHSearch fails on large predicted protein

Hi there,

Having set up `alphafold` in my machine (NVIDIA GeForce RTX 2080 GPU, ), which I've tested successfully, I'm now coming across the error below running it on a 5586 AA predicted protein (from a metagenome). I'm not sure what might be going wrong here as this seems like an internal `HHSearch` error.
I've tested this with the full and reduced `alphafold` databases on default parameters (just adding the output directory).
Thanks in advance for any help.

```
I0629 09:36:46.062932 139841260160832 run_docker.py:255] I0629 07:36:46.061630 139910991673152 utils.py:36] Started HHsearch query
I0629 09:36:46.688335 139841260160832 run_docker.py:255] I0629 07:36:46.687293 139910991673152 utils.py:40] Finished HHsearch query in 0.625 seconds
I0629 09:36:46.707670 139841260160832 run_docker.py:255] Traceback (most recent call last):
I0629 09:36:46.707909 139841260160832 run_docker.py:255] File "/app/alphafold/run_alphafold.py", line 422, in
I0629 09:36:46.708083 139841260160832 run_docker.py:255] app.run(main)
I0629 09:36:46.708291 139841260160832 run_docker.py:255] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run
I0629 09:36:46.708447 139841260160832 run_docker.py:255] _run_main(main, args)
I0629 09:36:46.708595 139841260160832 run_docker.py:255] File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main
I0629 09:36:46.708742 139841260160832 run_docker.py:255] sys.exit(main(argv))
I0629 09:36:46.708886 139841260160832 run_docker.py:255] File "/app/alphafold/run_alphafold.py", line 406, in main
I0629 09:36:46.709030 139841260160832 run_docker.py:255] random_seed=random_seed)
I0629 09:36:46.709173 139841260160832 run_docker.py:255] File "/app/alphafold/run_alphafold.py", line 174, in predict_structure
I0629 09:36:46.709334 139841260160832 run_docker.py:255] msa_output_dir=msa_output_dir)
I0629 09:36:46.709480 139841260160832 run_docker.py:255] File "/app/alphafold/alphafold/data/pipeline.py", line 188, in process
I0629 09:36:46.709624 139841260160832 run_docker.py:255] pdb_templates_result = self.template_searcher.query(uniref90_msa_as_a3m)
I0629 09:36:46.709766 139841260160832 run_docker.py:255] File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 96, in query
I0629 09:36:46.709911 139841260160832 run_docker.py:255] stdout.decode('utf-8'), stderr[:100_000].decode('utf-8')))
I0629 09:36:46.710054 139841260160832 run_docker.py:255] RuntimeError: HHSearch failed:
I0629 09:36:46.710198 139841260160832 run_docker.py:255] stdout:
I0629 09:36:46.710341 139841260160832 run_docker.py:255]
I0629 09:36:46.710483 139841260160832 run_docker.py:255]
I0629 09:36:46.710624 139841260160832 run_docker.py:255] stderr:
I0629 09:36:46.710766 139841260160832 run_docker.py:255] - 07:36:46.268 INFO: /tmp/tmpxkcxixk3/query.a3m is in A2M, A3M or FASTA format
I0629 09:36:46.710907 139841260160832 run_docker.py:255]
I0629 09:36:46.711049 139841260160832 run_docker.py:255] - 07:36:46.269 WARNING: Ignoring invalid symbol '*' at pos. 5586 in line 2 of /tmp/tmpxkcxixk3/query.a3m
I0629 09:36:46.711211 139841260160832 run_docker.py:255]
I0629 09:36:46.711354 139841260160832 run_docker.py:255] - 07:36:46.677 ERROR: [subseq from] Uncharacterized protein n=4 Tax=Candidatus Altiarchaeum TaxID=1803512 RepID=A0A1J5JGS9_9ARCH
I0629 09:36:46.711499 139841260160832 run_docker.py:255] - 07:36:46.677 ERROR: Error in /tmp/hh-suite/src/hhalignment.cpp:1244: Compress:
I0629 09:36:46.711654 139841260160832 run_docker.py:255]
I0629 09:36:46.711797 139841260160832 run_docker.py:255] - 07:36:46.677 ERROR: sequences in /tmp/tmpxkcxixk3/query.a3m do not all have the same number of columns,
I0629 09:36:46.711939 139841260160832 run_docker.py:255]
I0629 09:36:46.712081 139841260160832 run_docker.py:255] - 07:36:46.677 ERROR:
I0629 09:36:46.712221 139841260160832 run_docker.py:255] e.g. first sequence and sequence UniRef90_A0A1J5JGS9/19-5578.
I0629 09:36:46.712363 139841260160832 run_docker.py:255]
I0629 09:36:46.712503 139841260160832 run_docker.py:255] - 07:36:46.677 ERROR: Check input format for '-M a2m' option and consider using '-M first' or '-M 50'
```