AlphaFold multimer mode crashes with lower case protein sequences but not upper case protein sequences
This is by design, the sequences should be in all-uppercase letters, although I agree that AlphaFold should fail earlier and with a nicer error message.
In multimer mode, the following test sequence runs without error:

```
>HBA_HUMAN_2a Hemoglobin subunit alpha OS=Homo sapiens OX=9606 GN=HBA2 PE=1 SV=2
MALSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLS
HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFK
LLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
>HBB_HUMAN_2a Hemoglobin subunit beta OS=Homo sapiens OX=9606 GN=HBB PE=1 SV=2
MAHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLS
TPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVD
PENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
>HBA_HUMAN_2b Hemoglobin subunit alpha OS=Homo sapiens OX=9606 GN=HBA2 PE=1 SV=2
MALSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLS
HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFK
LLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
>HBB_HUMAN_2b Hemoglobin subunit beta OS=Homo sapiens OX=9606 GN=HBB PE=1 SV=2
MAHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLS
TPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVD
PENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
```

The same sequence, but just with lower case amino acids, causes AlphaFold to crash:

```
>HBA_HUMAN_2a Hemoglobin subunit alpha OS=Homo sapiens OX=9606 GN=HBA2 PE=1 SV=2
malspadktnvkaawgkvgahageygaealermflsfpttktyfphfdls
hgsaqvkghgkkvadaltnavahvddmpnalsalsdlhahklrvdpvnfk
llshcllvtlaahlpaeftpavhasldkflasvstvltskyr
>HBB_HUMAN_2a Hemoglobin subunit beta OS=Homo sapiens OX=9606 GN=HBB PE=1 SV=2
mahltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdls
tpdavmgnpkvkahgkkvlgafsdglahldnlkgtfatlselhcdklhvd
penfrllgnvlvcvlahhfgkeftppvqaayqkvvagvanalahkyh
>HBA_HUMAN_2b Hemoglobin subunit alpha OS=Homo sapiens OX=9606 GN=HBA2 PE=1 SV=2
malspadktnvkaawgkvgahageygaealermflsfpttktyfphfdls
hgsaqvkghgkkvadaltnavahvddmpnalsalsdlhahklrvdpvnfk
llshcllvtlaahlpaeftpavhasldkflasvstvltskyr
>HBB_HUMAN_2b Hemoglobin subunit beta OS=Homo sapiens OX=9606 GN=HBB PE=1 SV=2
mahltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdls
tpdavmgnpkvkahgkkvlgafsdglahldnlkgtfatlselhcdklhvd
penfrllgnvlvcvlahhfgkeftppvqaayqkvvagvanalahkyh
```

stderr:

```
I1108 11:39:45.759545 140705398323008 utils.py:40] Finished hmmbuild query in 0.248 seconds
I1108 11:39:45.767869 140705398323008 hmmsearch.py:103] Launching sub-process ['/usr/bin/hmmsearch', '--noali', '--cpu', '8', '--F1', '0.1', '--F2', '0.1', '--F3', '0.1', '--incE', '100', '-E', '100', '--domE', '100', '--incdomE', '100', '-A', '/mnt/alphafold/tmp/tmpug569gkx/output.sto', '/mnt/alphafold/tmp/tmpug569gkx/query.hmm', '/db/pdb_seqres/pdb_seqres.txt']
I1108 11:39:45.830403 140705398323008 utils.py:36] Started hmmsearch (pdb_seqres.txt) query
I1108 11:39:51.148423 140705398323008 utils.py:40] Finished hmmsearch (pdb_seqres.txt) query in 5.318 seconds
I1108 11:39:51.492158 140705398323008 jackhmmer.py:133] Launching subprocess "/usr/bin/jackhmmer -o /dev/null -A /mnt/alphafold/tmp/tmpwtlriesd/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /tmp/tmpuj71bpee.fasta /db/small_bfd/bfd-first_non_consensus_sequences.fasta"
I1108 11:39:51.550291 140705398323008 utils.py:36] Started Jackhmmer (bfd-first_non_consensus_sequences.fasta) query
I1108 11:43:15.578521 140705398323008 utils.py:40] Finished Jackhmmer (bfd-first_non_consensus_sequences.fasta) query in 204.028 seconds
I1108 11:43:15.585719 140705398323008 templates.py:940] Searching for template for: malspadktnvkaawgkvgahageygaealermflsfpttktyfphfdlshgsaqvkghgkkvadaltnavahvddmpnalsalsdlhahklrvdpvnfkllshcllvtlaahlpaeftpavhasldkflasvstvltskyr
Traceback (most recent call last):
  File "/app/alphafold/run_alphafold.py", line 422, in <module>
    app.run(main)
  File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/app/alphafold/run_alphafold.py", line 406, in main
    random_seed=random_seed)
  File "/app/alphafold/run_alphafold.py", line 174, in predict_structure
    msa_output_dir=msa_output_dir)
  File "/app/alphafold/alphafold/data/pipeline_multimer.py", line 269, in process
    is_homomer_or_monomer=is_homomer_or_monomer)
  File "/app/alphafold/alphafold/data/pipeline_multimer.py", line 214, in _process_single_chain
    msa_output_dir=chain_msa_output_dir)
  File "/app/alphafold/alphafold/data/pipeline.py", line 225, in process
    hits=pdb_template_hits)
  File "/app/alphafold/alphafold/data/templates.py", line 968, in get_templates
    kalign_binary_path=self._kalign_binary_path)
  File "/app/alphafold/alphafold/data/templates.py", line 727, in _process_single_hit
    query_sequence)
  File "/app/alphafold/alphafold/data/templates.py", line 657, in _build_query_to_hit_index_mapping
    min_idx = min(x for x in indices_query if x > -1)
ValueError: min() arg is an empty sequence
```