Did muscle v5 have sequence length limitation when align?

[overfly2067]

[align 13ncov.fa]
Input: 13 seqs, avg length 29840, max 30290, min 29527

WARNING: Long sequences, likey to crash / not globally alignable, max length is ~21k

00:00 4.3Mb 100.0% Derep 13 uniques, 0 dupes
00:00 4.3Mb CPU has 4 cores, running 4 threads

Sequence length 29666 >MW8 52494.1 Seve
Sere a
S
quence length 29802 >MG772933.1 Bat SARS-like coronavirus isolate bat-SL-CoVZC45, complete genome
Sequence length 29804 >MZ310903.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/SC-COVID21-1736/2021, complete genome

---Fatal error---
HMM overflow, sequence lengths 29802, 29804 (max ~21k)

The difficulty I met is above.Please help me,thank you!

[rcedgar]

As explained by the warning and error message these sequences are too long for muscle 5.
But, it's probably not a good idea to try to make an MSA from these nucleotide genomes, they are too far diverged.

[rcedgar]

if you want a pair-wise alignment, suggest try minimap

[overfly2067]

Thank you Mr. Robert!