Segmentation Fault after Loading Alignment

[Elizabeth Koning]

I am receiving a segfault when I try to run RAxML with my MSA. I would share the MSA as well, but it's 23G.

What are possible causes of this segfault? Is there a maximum input size I should limit myself to when using RAxML?

RAxML-NG v. 1.2.0 released on 09.05.2023 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: AMD EPYC 7551 32-Core Processor, 64 cores, 503 GB RAM

RAxML-NG was called at 24-Jul-2023 13:23:59 as follows:

raxml-ng --search1 --msa /home/erkonin/daily_notes/gene_trees/raxml/from_annotation/all_aln.fasta.raxml.reduced.phy --model GTR+G --threads 1

Analysis options:
  run mode: ML tree search
  start tree(s): parsimony (1)
  random seed: 1690230239
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  fast CLV updates: ON
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), NONE/sequential

[00:00:00] Reading alignment from file: /home/erkonin/daily_notes/gene_trees/raxml/from_annotation/all_aln.fasta.raxml.reduced.phy
[00:01:15] Loaded alignment with 91888 taxa and 268245 sites
/var/spool/slurmd/job20699/slurm_script: line 27: 88012 Segmentation fault      raxml-ng --search1 --msa $input_file --model GTR+G --threads 1

[Oleksiy Kozlov]

Hi Elizabeth,

could you please try

raxml-ng --parse --log debug --msa
/home/erkonin/daily_notes/gene_trees/raxml/from_annotation/all_aln.fasta.raxml.reduced.phy --model GTR+G

Best,
Oleksiy

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