Just to add I tested this on a bunch of public Eubacterium proteomes and got the same error, again based on an algnment with all “-”
>Eubacterium_limosum_strain_SA11
AVDGVSFTLNRSTLGIESCSTMGRSVLIEPTEQIYEEIMT
>Eubacterium_ruminantium_strain_ATCC_17233
VLKNINLKIREGMLGIRSASTLVNLISYDVNESLIDNVKD
>Eubacterium_sp_AB3007
----------------------------------------
>Eubacterium_oxidoreducens_strain_DSM_3217
ILKDVSFTIEPGKVALVNTSSLLR----------------
>Eubacterium_ruminantium_strain_HUN269
VLKNINLKIREGMLGIRSASTLVNLISYDVNESLIDNVKD
>Eubacterium_callanderi_strain_NLAE_zl_G225
AVDGVSFTLNRSTLGIESCSTMGRSVLIEPTEQIYEEIMT
>Eubacterium_ruminantium_strain_2388
VLKNINLKIREGMLGIRSASTLVNLISYDVNESLIDNVKD
>Eubacterium_uniforme_strain_ATCC_35992
AVKNVSFSVKKGTLGLESCTTVGKCVLYQITHKVFAEVYE
I just want to highlight I am running this with
–remove_fragmentary_entries --fragmentary_threshold 0.85