libc++abi: terminating with uncaught exception of type std::runtime_error: ERROR in SPR round (LIBPLL-3584): Constraint check failed after SPR round!

[rvosa]

I'm attempting the following constrained search:

raxml-ng --model GTR+G --outgroup GBMA5933-13,GBMNA13253-19,GBMA10242-15 --tree-constraint raxml-ready.tre --msa raxml-ready.fa --search

But this throws the exception:

libc++abi: terminating with uncaught exception of type std::runtime_error: ERROR in SPR round (LIBPLL-3584): Constraint check failed after SPR round!

Note sure what is going wrong here?

Input files:

• raxml-ready.fa.txt
• raxml-ready.tre.txt

Specs:

rutger@Rutgers-MacBook-Pro-2 9-of-17 % raxml-ng -h

RAxML-NG v. 1.1 released on 29.11.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz, 6 cores, 16 GB RAM

[amkozlov]

Could you please try to reproduce it with the most recent version:

https://github.com/amkozlov/raxml-ng/releases/tag/1.2.1

[rvosa]

Thanks for the response! I will try that but I guess that would mean that the bioconda version is kind of out of date. Might be worth pushing out a release there?

[amkozlov]

As of now, bioconda package is at v1.2.1:

https://anaconda.org/bioconda/raxml-ng

[jedgold]

I've had the same issue using 1.2.1:

terminate called after throwing an instance of 'std::runtime_error' what(): ERROR in SPR round (LIBPLL-3584): Constraint check failed after reinsert_nodes() in SPR round!

[pn023:142574] Process received signal [pn023:142574] Signal: Aborted (6) [pn023:142574] Signal code: (-6) [pn023:142574] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2aaaab83c630] [pn023:142574] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2aaaaba7f387] [pn023:142574] [ 2] /lib64/libc.so.6(abort+0x148)[0x2aaaaba80a78] [pn023:142574] [ 3] /lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x165)[0x2aaaab36fa95] [pn023:142574] [ 4] /lib64/libstdc++.so.6(+0x5ea06)[0x2aaaab36da06] [pn023:142574] [ 5] /lib64/libstdc++.so.6(+0x5ea33)[0x2aaaab36da33] [pn023:142574] [ 6] /lib64/libstdc++.so.6(+0xb53c5)[0x2aaaab3c43c5] [pn023:142574] [ 7] /lib64/libpthread.so.0(+0x7ea5)[0x2aaaab834ea5] [pn023:142574] [ 8] /lib64/libc.so.6(clone+0x6d)[0x2aaaabb47b0d] [pn023:142574] End of error message

[amkozlov]

Could you please try with v1.2.2:

https://github.com/amkozlov/raxml-ng/releases/tag/1.2.2

[fluttercork]

It looks like I'm getting at least partly a similar error (SPR round) except with branch lengths in a bootstrap optimisation:

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 -59510.203966771397972 units

Running raxml-ng 1.2.2 on macOS 14.5 on an M2 MacBook Air (8 cores, 24 GB RAM). Here's the call:

raxml-ng --msa strepsirrhini_batchNG.phylip --msa-format PHYLIP --data-type DNA --prefix strepsirrhini --redo --seed 4384 --model strepsirrhini_genePartitions.txt --all --bs-trees 1000 --tree rand{10},pars{10} --outgroup Tupaia_belangeri --threads auto{4} --workers auto{4}

The file has 44 partitions in it (individual genes, all set to GTR+G) and the call does work successfully with each individual gene.

[amkozlov]

@fluttercork thanks for reporting, but this is completely different error.

Which installation method have you used? We saw similar errors before on macOS/M2 due to (presumably) weird compilation issues. Can you reproduce the error with the pre-compiled binary?

https://github.com/amkozlov/raxml-ng/releases/download/1.2.2/raxml-ng_v1.2.2_macos.zip

[amkozlov]

Fixed in v1.2.2 as confirmed by @jedgold