AlphaFold fails in hhblits making sequence alignment

[Tom Goddard]

AlphaFold 2.1.1 fails with an error in hhblits, for example, with the sequence from PDB 7M1P

Error in /tmp/hh-suite/src/hhalignment.cpp:3539: MergeMasterSlave:
 	did not find 569 match states in sequence 1 of tr|A0A1H9CGJ3|A0A1H9CGJ3_9FIRM. Sequence:
 MVKVNGIRKTFGANEVLKGVSFEIEEGTIYGLIGRNGAGKTTLMNIMSGLLKADSGTFDMGTGKGSGKTQVGYLPDLPNFYDYLTTDEYLDFLLMESNPVRRDALLETVGLGKGLRIKTMSRGMKQRLGIAAVLVNDPKIILLDEPTSALDPAGRADVRSILMKLKSEGKTIILSTHILADMDSICDKAGFLAKGVIAREVNIAESRESASIMTISFASEPDLPTLHKYAPEIYIMDKCTIKIVLDKSDIITSQQKALQGLSQLPQEITSISSAALSLDNIFQEVCL

I attach the full alphafold log run on wynton. This error supposedly occurs only with full alphafold, not Google Colab which does not use hhblits. It has been reported to the Alphafold and hh-suite projects:

​https://github.com/deepmind/alphafold/issues/177

​https://github.com/soedinglab/hh-suite/issues/277

A suggested work-around is to update the UniClust database, although this probably just changes which sequences it fails on.

[Tom Goddard]

AlphaFold log with sequence alignment failure