GARD Internal error in _LikelihoodFunction::ConjugateGradientDescent

[tbigot]

Hi,

I’m having a problem running HYPHY with GARD. I have this kind of error:

Internal error in _LikelihoodFunction::ConjugateGradientDescent. The function evaluated at current parameter values [-6227879.055521984] does not match the last recorded LF maximum [-5227974.756559206]

My command: mpirun HYPHYMPI gard --type nucleotide --rv GDD --model JTT --rate-classes 4 --mode Faster --alignment nt.aln.fasta --output nt.aln.json

I can provide data or more complete logs if needed. Thanks in advance, Thomas

[spond]

Dear @tbigot,

Can you please let me know which HyPhy version you are using (hyphy --version or HYPHYMPI --version)?

Try adding `ENV="TOLERATE_NUMERICAL_ERRORS=1;" to your comman line call and see if that lets the job run to completion.

Would you be filling to share the input files with me (privately if needed) so that I could reproduce the error and try to resolve it more systematically?

Best, Sergei

[tbigot]

Thanks! I’m using the last GIT commit (41306280822033d0b6d9432cee8f7ed4051ee4d5) HYPHY 2.5.48(MPI) for Linux on x86_64.

It is public data, you’ll find them at: https://dl.pasteur.fr/fop/8NIIUfny/nt.aln.fasta.gz

[tbigot]

I can also provide the intermediate file generated by Gard, with the checkpoint data, it makes the software end a lot faster (because it re-uses the already computed results), if it helps! 🙂

[spond]

Dear @tbigot,

Sorry for letting this drop; can you please re-share the data.

Best, Sergei

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