MSA::SetIdCount: cannot increase count

[JAMKuttan]

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]

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

[JAMKuttan]

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]

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.

[moa4020]

Hello, I'm calling msa with "Muscle" multiple times in my script since it is part of a function for a pipeline I'm building. I am still facing this issue when I'm running msa for some reason:

> msa(c(primerSubset[primerName],stringSet),method="Muscle",type = "dna")

*** WARNING *** Assuming DNA (see -seqtype option), invalid letters found: 

*** ERROR ***  MSA::SetIdCount: cannot increase count

Fatal error, exception caught.
Error in msaFun(inputSeqs = inputSeqs, cluster = cluster, gapOpening = gapOpening,  : 
  MUSCLE finished by an unknown reason

Do you need additional information from my end to help resolve this issue?
I'm using msa Version 1.38.0

[UBod]

@moa4020, sorry for coming back to this issue so late! Yes, please send me a minimal example (code + data) that triggers this error. I will try to go through it and solve it.

[antoine4ucsd]

any update on this? I have the same issue - no problem in using muscle from terminal
thank you!

[UBod]

@antoine4ucsd, please send me a minimal example (code + data) that exposes this issue, and I will try to deal with it.

[antoine4ucsd]

I used muscle directly from the muscle R package instead.

[UBod]

@antoine4ucsd, that is too unspecific for debugging. Can you send a code snippet along with a FASTA sequence file that leads to this error in a fresh (vanilla) R session?