Alignment issue example on macOS-arm64 but not on linux server during refinement

[raufs]

Hi,

Thank you for developing FAMSA, it looks great!

I am seeing an error attempting to use FAMSA to align the below set of sequences on macOS-arm64 (M4 chip) that is not an issue on a standard Ubuntu server. For other cases it also can work fine on the macOS, but not this one for some reason. It gives a segmentation 11 error, here is the verbose output:

AMSA (Fast and Accurate Multiple Sequence Alignment)
  version 2.4.1-45c9b2b (2025-05-09)
  S. Deorowicz, A. Debudaj-Grabysz, A. Gudys

Aligning test_case/zol_Results/Ortholog_Group_Processing/OG_Protein_Sequences/OG_5.faa
Params:
  no. of threads: 6
  guide tree method: single linkage (MST+Prim)
  guide tree speeding up heuristic: None
  distance measure: indel075_div_lcs

Advanced params:
  no. of refinements: 100
  refinement threshold: 1000
  scroing matrix: PFASUM43
  gap open cost (rescalled): -14850
  gap extension cost (rescalled): -1250
  gap terminal open cost (rescalled): -660
  gap terminal extension cost (rescalled): -660
  gap cost scaller log-term: 45
  gap cost scaller div-term: 7
  enable gap rescaling: 1
  enable gap optimization: 1
  enable total score calculation: 1
  refinement mode: auto
  guided alignment radius: 50

Hardware configuration:
 Number of threads: 6
 Instruction set: None

Sorting sequences... [OK]
Duplicate removal... 5/6 sequences retained.
Computing guide tree... [OK]
Computing alignment...[OK]
Computing refinement...Segmentation fault: 11

With -refine_mode off it finishes successfully.

>Efaecalis_V583_fai-gene-cluster-1|AAC_002057
MGKVLNRIGRLILLVTMIGSYTMWVVGIDAPVTKYMYANSSILLLIAVILVLLLNCTKLKFIDWLTVALALATWLLFHFTESIRHSTMQTDTMIPLIILLVLCFKVCVFDRLDQTLLLIVSLVALSATLYRMSVELPQLIPADEIFKESNKLESIWINTNTIGATLMFSTMMASSLIKAYRNKVFNLLLLPVYIGGVLGTWVSQSKTSFAILVGFILVDNLLPKRFLQRSKVWLFGFVGVAALGPLLFYLCAESDTVDLFTGRERIWHEFFAKWLSDPQHIKVGMEPFVASWKPLGTHNAFLFTLSNFGVIGYLILFGFLVSMILLIGFRKKTLDRLQVSLLLGFLLIWIHSFMEDILLAPHWMPIVYSFLGLAFYFRPEKKRGRHERPTTPKRRKRVKQTSPVSNEERPIAPVDEEGWDQPEELSRVQRHRR
>Efaecium_EnGen0013_fai-gene-cluster-1|AAE_001513
MKIIQAIVQKFVNKMSVGFLLLLLTLVFFVWTAGVGFPATLFIYNNSSLLIAFSVAILLILNVYKAKGVDFLYLGVALALFIFFSYFRELRNESLFGDLLFPLIILFCLVIKWIEWTKWDRGIYLIVFTVFLGITLYRVFTEIQVPEGQSIWAPGNSLSDIWINTNTIGSSLMTLALLISGFASSFERWYVRIIGGIAVVAAFLGIWVCQSRGALVALIVFAILDLLPKSLMRVIRAPFIAYTVTILLALPISYLAAVSEKVNLFTGREDIWHKFYQTLGEKSEQVLLGMKTFIFQRGNQFLGNHNSYNSILNIYGLIGFGIAALLLILFIGRLTLKADLSNGQMTFIWAFFAVMMQSFMEDTLTSYPWVPIIYILLAMAVHRYDEPEVTEEFYVMEEAYDDMTYDDTSYEEQPDSAHSSRIQRYH
>Efaecium_EnGen0018_fai-gene-cluster-1|AAF_002022
MLVERRVEIIQAIVQKFVNKMSVGFLLLLLTLVFFVWTAGLGFPATLFIYNNSSLLIAFSVAILLILNVYKAKGVDFLYLGVALALFIFFSYFRELRNESLFGDLLFPLIILFCLVIKWIEWTKWDRGIYLIVFSVFLGITLYRVFTEIQVPEGQSIWAPGNSLSDIWINTNTIGSSLMTLALLISGFASSFERWYVRIIGAVAVVAAFLGIWVCQSRGALVALIVFAILDLLPKSLMRVIRAPFIAYTVTILLALPISYLAAVSEKVNLFTGREDIWHKFYQTLGEKSEQILLGMKTFIFQRGNQFLGNHNSYNSILNIYGLIGFGIAALLLILFIGRLTLKADLSNGQMTFIWAFFAVMMQSFMEDTLTSYPWVPIIYILLAMAVHRYDEPEVAEEFYVMEEAYDDMTYDDTSYEEQPDSAHSSRIQRYH
>Efaecalis_B594_fai-gene-cluster-1|AAA_002013
MGKVLNRIGRLILLVTMIGSYTMWVVGIDAPVTKYMYANSSILLLIAVILVLLLNCTKLKFIDWLTVALALATWLLFHFTESIRHSTMQTDTMIPLIILLVLCFKVCVFDRLDQTLLLIVSLVALSATLYRMSVELPQLIPADEIFKESNKLESIWINTNTIGATLMFSTMMASSLIKAYRNKVFNLLLLPVYIGGVLGTWVSQSKTSFAILVGFILVDNLLPKRFLQRSKVWLFGFVGVAALGPLLFYLCAESDTVDLFTGRERIWHEFFAKWLSDPQHIKVGMEPFVASWKPLGTHNAFLFTLSNFGVIGYLILFGFLVSMILLIGFRKKTLDRLQVSLLLGFLLIWIHSFMEDILLAPHWMPIVYSFLGLAFYFRPEKKRGRHERPTTPKRRKRVKQTSPVSNEERPIAPVDEEGWDQPEELSRVQRHRR
>Efaecium_EnGen0003_fai-gene-cluster-1|AAD_000104
MLLLLTLVFSVWTAGLSFPTTLFIYNNSSLLITFSVAILLILNVYKAKGVDFLYLGVALALFIFFSYFRELRNESLFGDLLFPLIILFCLVIKWIEWTKWDRGIYLLVFTVFLGITLYRVFTEIQVPEGQSIWTPGNSLSDIWINTNTIGSSLMTLALLISGFASSFERWYVRIIGAIAVVAAFLGIWVCQSRGALVALIVFAILDLFPKSLMRVIRAPFIAYTATILLALPISYLAAVSEKVNLFTGREDIWHKFYQTLGEKSEQVLLGMKTFIFQRGNQFLGNHNSYNSILNIYGLIGFGIAALLLILFIGRLTLKADLSNGQMTFIWAFFAVMMQSFMEDTLTSYPWVPIIYILLAMAVHRYDETKVMEEYYDIEEPYDDMNAGDPSYEEQPDSAHSSRIQRYH
>Efaecalis_OG1RF_fai-gene-cluster-1|AAB_001674
MGKVLNRIGRLILLVTMIGSYTMWVVGIDAPVTKYMYANSSILLLIAVILVLLLNCTKLKFIDWLTVALALATWLLFHFTESIRHSTMQTDTMIPLIILLVLCFKVCVFDRVDQTLLLIVSLVALSATLYRMSVELPQLIPADEIFKESNKLESIWINTNTIGATLMFSTMMASSLIKAYRNKVFNLLLLPVYIGGVLGTWVSQSKTSFAILVGFILVDNLLPKRFLQRSKVWLFGFVGVAALGPLLFYLCAESDTVDLFTGRERIWHEFFAKWLSDPQHIKVGMEPFVASWKPLGTHNAFLFTLSNFGVIGYLILFGFLVSMILLIGFRKKTLDRLQVSLLLGFLLIWIHSFMEDILLAPHWMPIVYSFLGLAFYFRPEKKRGRHESPTTPKRRKRVKQTSPVSNEERPIAPVDEEGWDQPEELSRVQRHRR

Kind regards,
Rauf