Constrained optimization failed, since a starting point within the domain specified for the variables couldn't be found. Failed constraint:relax.ge.omega2

[fuesseler]

Dear Hyphy Team, Thanks for developing and maintaining this great set of tools! I've been trying to run RELAX on ~14k ortholog alignments, from 6 species.

I installed the newest version from source: HYPHY 2.5.62(MP) for Linux on x86_64 x86 SSE4 SIMD zlib (v1.2.11) (had to turn off AVX support due to our cluster architecture)

Unfortunately, I get the following error for some alignments:

Error: Internal error Constrained optimization failed, since a starting point within the domain specified for the variables couldn't be found. Set it by hand, or check your constraints for compatibility. Failed constraint:relax.ge.omega2:=1/0.4549925633717588 must be in [0,10000]. Current value = 1.

The command I run as such: $HYPHY ENV="TOLERATE_NUMERICAL_ERRORS=1;" relax --alignment ${INDIR}/"$outname".pal2nal.clipkit.aln.renamed --tree ${TREEDIR}/"$outname".lb.tree --test Foreground --reference Background --srv Yes --output ${OUTDIR}/"${outname}.srv_gt.RELAX.json" > ${OUTDIR}/"${outname}.srv_sptree.RELAX.log" 2>&1 The same alignments work fine when I am running ABSREL on them.

Do you have any suggestions on what I might try for these to work? I would be grateful for any insights!