Gene-tree generation

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Wyclif Odago

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Nov 4, 2023, 7:16:06 AM11/4/23
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Hi, I have a set of 353 genes for about 120 species. I want to generate gene trees for each gene using RAxML-NG. Is there a specific command that can run all the gene trees at once without doing it one by one for all 353 gene sets?
Thanks.

Alexandros Stamatakis

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Nov 5, 2023, 1:21:17 AM11/5/23
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Dear Wyclif,

We have developed a dedicated tool exactly for this:

https://academic.oup.com/bioinformatics/article/35/10/1771/5132696

Alexis
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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

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

Wyclif Odago

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Nov 6, 2023, 2:53:18 AM11/6/23
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Hello,
Thank you for the help. I run the analysis but bumped into an error "what():  ERROR in SPR round (LIBPLL-2240): BL opt converged to a worse likelihood score by -0.020301299073765 units" during subtree pruning and regrafting (SPR). Since the optimiztion step did not converge how do I correct this? Of course I re-checked the alignment but the error keeps repeating. 
Thanks.

Oleksiy Kozlov

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Nov 6, 2023, 5:06:52 AM11/6/23
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Hi Wyclif,

please make sure you are using the latest raxml-ng version, and add "--blopt nr_safe" parameter.

Best,
Oleksiy
> <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>>.
>
> --
> 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> (Crete lab)
> www.exelixis-lab.org <http://www.exelixis-lab.org> (Heidelberg lab)
>
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Chase W. Nelson

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Jan 27, 2024, 1:54:56 AMJan 27
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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.

Thanks so much!
Chase

Chase W. Nelson

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Jan 27, 2024, 1:54:56 AMJan 27
to raxml
Greetings!

I seem to be generating at least two similar errors, depending on the random seed. For both errors (below), using --blopt nr_safe at best delays the crash. N.B. I just installed raxml-ng v1.2.1 using homebrew on Mac, and 100% of the Quick Start tutorial runs without issue.

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 --seed 2 --blopt nr_safe

blopt error mentioned in this thread (when using --seed 2):
...
[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
 

Assertion failed error (when using --seed 1):
...
[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
 

This ignorant popgen guy would be grateful for any ideas! (Can de-identify alignment and share privately if helpful.)

Thanks so much!
Chase
On Monday, November 6, 2023 at 5:06:52 AM UTC-5 Oleksiy Kozlov wrote:

Alexandros Stamatakis

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Jan 27, 2024, 2:41:48 AMJan 27
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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>>
> (Heidelberg lab)
> >
> > --
> > You received this message because you are subscribed to the
> Google Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send an email to
> > raxml+un...@googlegroups.com <mailto:raxml+un...@googlegroups.com>.
> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/raxml/f923a170-7b5c-458a-accf-3e2867d4d694n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/f923a170-7b5c-458a-accf-3e2867d4d694n%40googlegroups.com>
> >
> <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>>.
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
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> <mailto:raxml+un...@googlegroups.com>.
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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

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