Error while running Raxml-ng

[Ufungi]

Dear author,

I ran rappas on linux system with 256 GB RAM and 32 cores (64 threads).

The run failed with the error below

rappas -p b -s nucl -w /home/snyoo/pp_result/rappas/db/ -b /home/snyoo/miniconda3/bin/raxml-ng -r /data/snyoo/DB/WITCH-NG/target/release/UNITE_witch_ng.afa -t /data/snyoo/DB/WITCH-NG/target/release/UNITE_witch_ng.nwk --no-reduction -v 1 --force-root --threads 16
wordDir: /home/snyoo/pp_result/rappas/db
Using AR binary provided by user: /home/snyoo/miniconda3/bin/raxml-ng
Original alignment will be used (no gapped columns removed).
Default k=8 will be used.
Default omega=1.5 will be used.
Default ratio-reduction=0.99 will be used.
Default injectionPerBranch=1 will be used.
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RAPPAS v1.21

---------------------------------------------

Rapid Alignment-free Phylogenetic Placement

via Ancestral Sequences

Linard B, Swenson KM, Pardi F

LIRMM, Univ. of Montpellier, CNRS, France

https://doi.org/10.1101/328740

benjamin/dot/linard/at/lirmm/dot/fr

################################################
workDir=/home/snyoo/pp_result/rappas/db
Starting db_build pipeline...
Set analysis for DNA
User did not set model parameters, using default: m=GTR;a=1.0;c=4;
main_v2.Main_DBBUILD_3--> k=8
main_v2.Main_DBBUILD_3--> factor=1.5
main_v2.Main_DBBUILD_3--> PPStarThreshold=3.9106607E-4
main_v2.Main_DBBUILD_3--> log10(PPStarThreshold)=-3.40775
main_v2.Main_DBBUILD_3--> Loading alignment: /data/snyoo/DB/WITCH-NG/target/release/UNITE_witch_ng.afa
Some ambiguous states were found in the alignment. (use '-v 1' to know more)
alignement.Alignment--> Ambiguous state: char='B' occurences=1
alignement.Alignment--> Ambiguous state: char='d' occurences=1
alignement.Alignment--> Ambiguous state: char='D' occurences=2
alignement.Alignment--> Ambiguous state: char='H' occurences=2
alignement.Alignment--> Ambiguous state: char='K' occurences=177
alignement.Alignment--> Ambiguous state: char='k' occurences=22
alignement.Alignment--> Ambiguous state: char='M' occurences=140
alignement.Alignment--> Ambiguous state: char='m' occurences=16
alignement.Alignment--> Ambiguous state: char='N' occurences=1047
alignement.Alignment--> Ambiguous state: char='n' occurences=178
alignement.Alignment--> Ambiguous state: char='R' occurences=575
alignement.Alignment--> Ambiguous state: char='r' occurences=31
alignement.Alignment--> Ambiguous state: char='S' occurences=141
alignement.Alignment--> Ambiguous state: char='s' occurences=14
alignement.Alignment--> Ambiguous state: char='v' occurences=1
alignement.Alignment--> Ambiguous state: char='V' occurences=2
alignement.Alignment--> Ambiguous state: char='W' occurences=198
alignement.Alignment--> Ambiguous state: char='w' occurences=21
alignement.Alignment--> Ambiguous state: char='Y' occurences=1023
alignement.Alignment--> Ambiguous state: char='y' occurences=49
main_v2.Main_DBBUILD_3--> Alignment read: Dimension: 38208x28381 (colxline)
main_v2.Main_DBBUILD_3--> Gap ratio: 69.73624883831596
main_v2.Main_DBBUILD_3--> >=0.3, gap jumps activated.
main_v2.Main_DBBUILD_3--> Loading tree: /data/snyoo/DB/WITCH-NG/target/release/UNITE_witch_ng.nwk
tree.NewickReader--> Rooting of input unrooted Tree !
tree.PhyloTree--> Building tree indexation
main_v2.Main_DBBUILD_3--> Original tree read.
tree.PhyloTree--> Building tree indexation
Injecting fake nodes...
tree.PhyloTree--> Building tree indexation
tree.ExtendedTree--> # nodes in tree before extension: 56761
tree.ExtendedTree--> # nodes in tree after extension: 283801
tree.PhyloTree--> Building tree indexation
main_v2.Main_DBBUILD_3--> RelaxedTree contains 141901 leaves
main_v2.Main_DBBUILD_3--> RelaxedTree contains 113520 FAKE_X new leaves
main_v2.Main_DBBUILD_3--> Write extended alignment (fasta): /home/snyoo/pp_result/rappas/db/extended_trees/extended_align.fasta
main_v2.Main_DBBUILD_3--> Write extended alignment (phylip): /home/snyoo/pp_result/rappas/db/extended_trees/extended_align.phylip
main_v2.Main_DBBUILD_3--> Write extended newick tree: /home/snyoo/pp_result/rappas/db/extended_trees/extended_tree_withBL.tree
main_v2.Main_DBBUILD_3--> Write extended newick tree with branch length: /home/snyoo/pp_result/rappas/db/extended_trees/extended_tree_withBL_withoutInterLabels.tree
main_v2.Main_DBBUILD_3--> Storing binary version of Extended Tree.
I guess, from binary name, we are using RAXML-NG.
Launching ancestral reconstruction...
inputs.ARProcessLauncher--> RAXML-NG AR was selected.
inputs.ARProcessLauncher--> Ancestral reconstruct command: [/home/snyoo/miniconda3/bin/raxml-ng, --ancestral, --msa, /home/snyoo/pp_result/rappas/db/extended_trees/extended_align.phylip, --tree, /home/snyoo/pp_result/rappas/db/extended_trees/extended_tree_withBL_withoutInterLabels.tree, --threads, 16, --redo, --precision, 9, --seed, 1, --force, msa, --data-type, DNA, --model, GTR+G4{1.0}+IU{0}+FC, --blopt, nr_safe, --opt-model, on, --opt-branches, on]
inputs.ARProcessLauncher--> Current directory:/home/snyoo/pp_result/rappas/db/AR
inputs.ARProcessLauncher--> External process operating reconstruction is logged in: /home/snyoo/pp_result/rappas/db/AR/AR_sdtout.txt
inputs.ARProcessLauncher--> Launching ancestral reconstruction (go and take a coffee, it might take hours if > 5000 leaves!) ...
Output from external software:

RAxML-NG v. 1.0.1 released on 19.09.2020 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
RAxML-NG was called at 12-Apr-2023 17:02:56 as follows:

/home/snyoo/miniconda3/bin/raxml-ng --ancestral --msa /home/snyoo/pp_result/rappas/db/extended_trees/extended_align.phylip --tree /home/snyoo/pp_result/rappas/db/extended_trees/extended_tree_withBL_withoutInterLabels.tree --threads 16 --redo --precision 9 --seed 1 --force msa --data-type DNA --model GTR+G4{1.0}+IU{0}+FC --blopt nr_safe --opt-model on --opt-branches on

Analysis options:
run mode: Ancestral state reconstruction
start tree(s): user
random seed: 1
tip-inner: ON
pattern compression: OFF
per-rate scalers: OFF
site repeats: OFF
branch lengths: proportional (ML estimate, algorithm: NR-SAFE)
SIMD kernels: AVX2
parallelization: coarse-grained (auto), PTHREADS (16 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /home/snyoo/pp_result/rappas/db/extended_trees/extended_align.phylip

Alignment comprises 1 partitions and 38208 sites

NOTE: Binary MSA file created: /home/snyoo/pp_result/rappas/db/extended_trees/extended_align.phylip.raxml.rba

Parallel reduction/worker buffer size: 1 KB / 0 KB

[00:01:12] Loading user starting tree(s) from: /home/snyoo/pp_result/rappas/db/extended_trees/extended_tree_withBL_withoutInterLabels.tree
[00:01:14] Data distribution: max. partitions/sites/weight per thread: 1 / 2388 / 38208
[00:01:14] Data distribution: max. searches per worker: 1

Starting ML tree search with 1 distinct starting trees

Ancestral reconstruction finished. Return to RAPPAS process.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!! Raxml-ng outputs are missing, the process may have failed... !!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Some clues may be found in the AR/AR_sdterr.txt or AR/AR_sdtour.txt files.

AR_sdtout.txt
AR_sdterr.txt

I couldn't find out any error messages in the txt files.

Thank you in advance for your assistance.

Best regards,

Shinnam Yoo