hhblits crashing with Error did not find 548 match states in sequence

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Expected Behavior

hhblits does not crash on this sequence:

>Q13838_DX39B_HUMAN
MAENDVDNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIEQTR

and using uniclust30_2018_08 database.

Current Behavior

hhblits crashes with the error:

...
- 13:20:30.255 INFO: Realigning 33501 HMM-HMM alignments using Maximum Accuracy algorithm

- 13:34:59.564 ERROR: Error in /tmp/eb-build/HHsuite/3.3.0/gompic-2020b/hh-suite-3.3.0/src/hhalignment.cpp:3539: MergeMasterSlave:

- 13:34:59.564 ERROR:   did not find 548 match states in sequence 1 of SRR5579859_7281350. Sequence:
 PGLGQNGAMPGIAWFKLTDPGGELPAVSSDTDLRILLPEGDEFGIQARRLADAGAQVRQVRYLLEDEAITGEGKRREVITWLSRPSQPGGGPYAKVTGPATTGARDAFELMWQDQALPIGQAAMRTRVPAVLAAFLPFSTLNPAQAEIVPEVLGHDQNLLVVAPTGAGKTVIGMAAGLKAVLEQKRKAAWLVPQRSLTDELDRELADWRGRGLRVERLSGE

There are also some other sequences crashing like this, can provide them if useful

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps.

hhblits -i crashing_seq.fasta -cpu 12 -oa3m /scratch/kosinski/output.a3m -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /scratch/AlphaFold_DBs/2.2.0/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /scratch/AlphaFold_DBs/2.2.0/uniclust30/uniclust30_2018_08/uniclust30_2018_08

HH-suite Output (for bugs)

Please make sure to post the complete output of the tool you called. Please use gist.github.com.

Context

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Your Environment

Include as many relevant details about the environment you experienced the issue in.

Version/Git commit used: Version 3.3.0 and the current git master. version 3.0 crashes too.
Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
Operating system and version: Liux CentOS

soedinglab / hh-suite