using MSA from HHblits

## Expected Behavior
Trying to use the custom MSA option using HHBlits (https://toolkit.tuebingen.mpg.de/jobs/RSC30_1).
I followed the instructions and downloaded the a3m file

ColabFold input

sequence:
MMDMQVRKVRKPPACTQCRKRKIGCDRAKPICGNCVKYNKPDCFYPDGPGKMVAVPSASGMSTHGNGQGSNHFSQGNGVNQKNVMIQTQYPIMQTSIEAFNFSFNPSVDTAMQWTKAASYQNNNTNNNTAPRQNSSTVSSNVHGNTIVRSDSPDVPSMDQIREYNTRLQLVNAQSFDYTDNPYSFNVGINQDSAVFDLMTSPFTQEEVLIKEIDFLKNKLLDLQSLQLKSLKEKSNLNADNTTANKINKTGENSKKGKVDGKRAGFDHQTSRTSQSSQKYFTALTITDVQSLVQVKPLKDTPNYLFTKNFIIFRDHYLFKFYNILHDICHINQFKVSPPNNKNHQQYMEVCKVNFPPKAIIIETLNSESLNNLNIEEFLPIFDKTLLLEFVHNSFPNGDTCPSFSTVDLPLSQLTKLGELTVLLLLLNDSMTLFNKQAINNHVSALMNNLRLIRSQITLINLEYYDQETIKFIAITKFYESLYMHDDHKSSLDEDLSCLLSFQIKDFKLFHFLKKMYYSRHSLLGQSSFMVPAAENLSPIPASIDTNDIPLIANDLKLLETQAKLINILQGVPFYLPVNLTKIESLLETLTMGVSNTVDLYFHDNEVRKEWKDTLNFINTIVYTNFFLFVQNESSLSMAVQHSSNNNKTSNSERCAKDLMKIISNMHIFYSITFNFIFPIKSIKSFSSGNNRFHSNGKEFLFANHFIEILQNFIAITFAIFQRCEVILYDEFYKNLSNEEINVQLLLIHDKILEILKKIEIIVSFLRDEMNSNGSFKSIKGFNKVLNLIKYMLRFSKKKQNFARNSDNNNVTDYSQSAKNKNVLLKFPVSELNRIYLKFKEISDFLMEREVVQRSIIIDKDLESDNLGITTANFNDFYDAFYN

a3m file attached

ColabFold Output (for bugs)

2022-01-03 12:51:39,739 Running colabfold 1.2.0 (f5d0cec9e4045666cb615ec9ad89b3bdc1ecda62)
2022-01-03 12:51:39,742 Found 4 citations for tools or databases
2022-01-03 12:51:48,037 Query 1/1: testRSC30_d0060.custom (length 883)
2022-01-03 12:51:48,043 Could not generate input features testRSC30_d0060.custom: list index out of range
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 1046, in run
model_type,
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 757, in generate_input_feature
sequence, input_msa, template_features[sequence_index]
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 624, in build_monomer_feature
msa = pipeline.parsers.parse_a3m(unpaired_msa)
File "/usr/local/lib/python3.7/dist-packages/alphafold/data/parsers.py", line 170, in parse_a3m
sequences, descriptions = parse_fasta(a3m_string)
File "/usr/local/lib/python3.7/dist-packages/alphafold/data/parsers.py", line 89, in parse_fasta
sequences[index] += line
IndexError: list index out of range
2022-01-03 12:51:48,043 Done

Your Environment

AlphaFold2 Colab notebook

hhblits_fullQT_RSC30_1.txt

Start with colabfold/batch.py at build_monomer_feature and generate_input_feature, then inspect alphafold/data/parsers.py: parse_a3m and the attached hhblits output. Reproduce the custom-MSA run and determine why the A3M parser reaches an invalid sequence index. Done means the supplied HHblits A3M is accepted and feature generation completes without the IndexError.