Bug report: substitution model

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Cedric Chauve

Mar 26, 2023, 5:58:38 PM3/26/23
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I am trying to run BAli-Phy on the coding sequences of a few mosquito genes.

I am running BAli-Phy VERSION: 4.0-beta2

The command line I run is
bali-phy OG6_100154.fasta --package-path /scratch/chauvec/bali-phy/lib/bali-phy/ -S tn93+Rates.gamma+inv
The error message I receive is
bali-phy: Error! Command 'Rates.gamma' missing required argument 'submodel'

Cedric Chauve

Benjamin Redelings

Mar 27, 2023, 9:18:53 AM3/27/23
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Hi Cedric,

I checked that this command works on the binaries of 4.0-beta2 released
on github.

Did you by chance compile from source in the last few days?  If so, then
you've probably included some changes towards 4.0-beta3 that are not
released yet.  I've changed the version number to 4.0-beta3-preview and
modified the NEWS file to reflect this.

The simplest thing might be to just replace '+' with '+>':

bali-phy OG6_100154.fasta --package-path /scratch/chauvec/bali-phy/lib/bali-phy/ -S 'tn93+>Rates.gamma+>inv'

You will also need to put the substitution model in quotes, since the
shell will otherwise eat the '>' character.  Alternatively, you could
run 'git checkout 4.0-beta2' to go back to 4.0-beta2, which still allows
the old syntax.

BTW, usually it is not necessary to specify the package path, since
bali-phy can figure it out relative to the location of the bali-phy
executable.  Is that not working for you?

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