id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6105	AlphaFold fails in hhblits making sequence alignment	Tom Goddard	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."	defect	assigned	moderate		Structure Prediction				mtrnka@…				all	ChimeraX