Hi Chase,
Thanks for reporting, it would be good if you could share the
de-identified data with Alexey. He's just teaching at a summer school
right now so it might take him some time to respond.
Alexis
On 26.01.24 23:24, Chase W. Nelson wrote:
> Greetings!
>
> I just installed raxml-ng v1.2.1 via homebrew on Mac. All of the Quick
> Start tutorial runs without issue.
>
> I seem to be generating errors related to the above discussion, with
> specifics depending on the random seed. Using --blopt nr_safe at best
> delays the crash. Some of the time no crash occurs at all; while I could
> just use the successful runs, I'm worried that would bias results in
> some way.
>
> *_Specs:_*
> RAxML-NG v. 1.2.1-master released on 22.12.2023 by The Exelixis Lab.
> Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
> Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah
> Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
> Latest version:
https://github.com/amkozlov/raxml-ng
> Questions/problems/suggestions? Please visit:
>
https://groups.google.com/forum/#!forum/raxml
>
> System: Apple M2 Max, 12 cores, 96 GB RAM
>
> *_Command:_*
> raxml-ng --search1 --msa P.raxml.rba --model GTR+G --prefix T --threads 5
>
> *_Error 1 (--seed 1_**_):_*
> [00:00:52 -22359.646741] SLOW spr round 1 (radius: 5)
> [00:00:58 -22359.623992] SLOW spr round 2 (radius: 10)
> [00:01:05 -22359.621547] SLOW spr round 3 (radius: 15)
> Assertion failed: (new_loglikeliAssertion failed:
> (new_loglikeliAssertion failed: (new_loglikelihood - loglikelihood >
> new_loglihood - loglikelihood > new_loglihood - loglikelihood >
> new_loglikelihood * BETTER_LL_TRESHOLD), kelihood * BETTER_LL_TRESHOLD),
> Assertion failed: (new_loglikelifunction pllmod_opt_optimize_brakelihood
> * BETTER_LL_TRESHOLD), function
> pllmod_opt_optimize_branch_lengths_local_multi, file plfunction
> pllmod_opt_optimize_branch_lengths_local_multi, file pll_optimize.c,
> line 1903.
> nch_lengths_local_multi, file pll_optimize.c, line 1903.
> l_optimize.c, line 1903.
> hood - loglikelihood > new_loglikelihood * BETTER_LL_TRESHOLD), function
> pllmod_opt_optimize_branch_lengths_local_multi, file pll_optimize.c,
> line 1903.
> zsh: abort raxml-ng --search1 --msa P.raxml.rba --model GTR+G
> --prefix T --threads 5 2
> *_
> _*
> *_Error 2 (--seed 2):_*
> [00:00:32 -22361.451487] Model parameter optimization (eps = 1.000000)
> [00:00:32 -22361.446547] SLOW spr round 1 (radius: 5)
> [00:00:37 -22360.379097] SLOW spr round 2 (radius: 10)
> Assertion failed: (new_loglikelihood - loglikelihood > new_loglikelihood
> * BETTER_LL_TRESHOLD), function
> pllmod_opt_optimize_branch_lengths_local_multi, file pll_optimize.c,
> line 1903.
> zsh: abort raxml-ng --search1 --msa P.raxml.rba --model GTR+G
> --prefix T --threads 5 1
>
> *_Error 3 (--seed 1706307277):_*
> ...
> [00:00:39 -22364.461723] SLOW spr round 3 (radius: 15)
> [00:00:51 -22363.663905] SLOW spr round 4 (radius: 20)
> [00:01:14 -22363.663804] SLOW spr round 5 (radius: 25)
> libc++abi: terminating due to uncaught exception of type
> std::runtime_error: ERROR in SPR round (LIBPLL-2240): BL opt converged
> to a worse likelihood score by -4749.869578142792307 units
> libc++abi: terminating due to uncaught exception of type
> std::runtime_error: ERROR in SPR round (LIBPLL-2240): BL opt converged
> to a worse likelihood score by -4749.869578142792307 unitslibc++abi:
> terminating due to uncaught exception of type std::runtime_error: ERROR
> in SPR round (LIBPLL-2240): BL opt converged to a worse likelihood score
> by -4749.869578142792307 unitslibc++abi: terminating due to uncaught
> exception of type std::runtime_error: ERROR in SPR round (LIBPLL-2240):
> BL opt converged to a worse likelihood score by -4749.869578142792307 units
>
> zsh: abort raxml-ng --search1 --msa P.raxml.rba --model GTR+G --prefix T
> --threads 5
>
> *_Error 4 (--seed 1706307277, add --blopt nr_safe)_*
> [00:00:24 -22373.568542] FAST spr round 1 (radius: 15)
> [00:00:29 -22364.808395] Model parameter optimization (eps = 1.000000)
> [00:00:30 -22364.772547] SLOW spr round 1 (radius: 5)
> Assertion failed: (new_loglikeliAssertion failed:
> (new_loglikeliAssertion failed: (new_loglikeliAssertion failed:
> (new_loglikelihood - loglikelihood > new_loglihood - loglikelihood >
> new_loglikelihood * BETTER_LL_TRESHOLD), function
> pllmod_opt_optimize_brahood - loglikelihood >
> new_loglinch_lengths_local_multi, file plAssertion failed:
> (new_loglikelikelihood * BETTER_LL_TRESHOLD), function
> pllmod_opt_optimize_brahood - loglikelihood >
> new_loglinch_lengths_local_multi, file plhood - loglikelihood >
> new_loglikelihood * BETTER_LL_TRESHOLD), kelihood * BETTER_LL_TRESHOLD),
> l_optimize.c, line 1903.
> kelihood * BETTER_LL_TRESHOLD), function pllmod_opt_optimize_brafunction
> pllmod_opt_optimize_branch_lengths_local_multi, file pll_optimize.c,
> line 1903.
> nch_lengths_local_multi, file pll_optimize.c, line 1903.
> l_optimize.c, line 1903.
> function pllmod_opt_optimize_branch_lengths_local_multi, file
> pll_optimize.c, line 1903.
> zsh: abort raxml-ng --search1 --msa P.raxml.rba --model GTR+G
> --prefix T --threads 5
>
> Your resident popgen ignoramous would be grateful for any help! Can
> privately share de-identified data if it would be of use.*_
> _*
> <
https://groups.google.com/d/msgid/raxml/53f00970-413a-4b0c-9eec-33f8efc21348n%40googlegroups.com <
https://groups.google.com/d/msgid/raxml/53f00970-413a-4b0c-9eec-33f8efc21348n%40googlegroups.com>> <
https://groups.google.com/d/msgid/raxml/53f00970-413a-4b0c-9eec-33f8efc21348n%40googlegroups.com?utm_medium=email&utm_source=footer <
https://groups.google.com/d/msgid/raxml/53f00970-413a-4b0c-9eec-33f8efc21348n%40googlegroups.com?utm_medium=email&utm_source=footer> <
https://groups.google.com/d/msgid/raxml/53f00970-413a-4b0c-9eec-33f8efc21348n%40googlegroups.com?utm_medium=email&utm_source=footer <
https://groups.google.com/d/msgid/raxml/53f00970-413a-4b0c-9eec-33f8efc21348n%40googlegroups.com?utm_medium=email&utm_source=footer>>>.
> >
> > --
> > Alexandros (Alexis) Stamatakis
> >
> > ERA Chair, Institute of Computer Science, Foundation for Research
> and
> > Technology - Hellas
> > Research Group Leader, Heidelberg Institute for Theoretical Studies
> > Full Professor, Dept. of Informatics, Karlsruhe Institute of
> Technology
> >
> >
www.biocomp.gr <
http://www.biocomp.gr> <
http://www.biocomp.gr
> <
http://www.exelixis-lab.org <
http://www.exelixis-lab.org>>
> <
https://groups.google.com/d/msgid/raxml/f923a170-7b5c-458a-accf-3e2867d4d694n%40googlegroups.com?utm_medium=email&utm_source=footer <
https://groups.google.com/d/msgid/raxml/f923a170-7b5c-458a-accf-3e2867d4d694n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
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--
Alexandros (Alexis) Stamatakis
ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology