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UBod / msa

R package for multiple sequence alignment
https://github.com/UBod/msa
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MSA::SetIdCount: cannot increase count #30

Closed JAMKuttan closed 3 weeks ago

JAMKuttan commented 1 month ago

I am running msa with method set to Muscle. Most of the times it works but sometimes I get error: ERROR MSA::SetIdCount: cannot increase count

Not sure what is happening here or why this is being triggered. my code: msa <- msa::msa(dnaSS, method = "Muscle", gapExtension = 73, type = "dna", order = "input")

JAMKuttan commented 1 month ago

What is even more curious is I find if I remove 3-4 reads at random the algorithm works.

JAMKuttan commented 1 month ago

Seems to be triggered here but I am not sure what this is meant for.. https://github.com/UBod/msa/blob/devel/src/Muscle/msa.cpp#L656

UBod commented 3 weeks ago

Thanks for reporting this issue, @JAMKuttan! It turned out that the same issue had been discussed on https://www.biostars.org/p/438744/ before, but I only found it now.

The point is that there was a major bug in the Muscle interface that - to my deepest regret - had not been discovered so far: If you run Muscle more than once, you can only run it with no more sequences than in the first call. The solution was not that trivial, but I tried my best. A new version (1.37.3) has been pushed to this repo and the BioC devel branch now. I hope this closes this issue. If you encounter any further problems, please reopen this issue or open a new one.