raxml-ng 1.2.0 Segmentation Faul

[Renato Oliveira]

Hey all!

Can anyone help me with this Segmentation Fault problem? 

Here goes the log:

raxml-ng --evaluate --msa data/rbcL_ITS2_alignment_resolved.fasta --tree data/APG4_PFC_equal.resolved.newick --model GTR+G --prefix test/model/model_eval --threads 4 --log debug

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: Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz, 2 cores, 12 GB RAM

RAxML-NG was called at 29-May-2023 01:43:39 as follows:

/mnt/c/Dados/softwares/raxml-ng/raxml-ng --evaluate --msa data/rbcL_ITS2_alignment_resolved.fasta --tree data/APG4_PFC_equal.resolved.newick --model GTR+G --prefix test/model/model_eval --threads 4 --log debug

Analysis options:
  run mode: Evaluate tree likelihood
  start tree(s): user
  random seed: 1685335419
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF

RBA partial loading: OFF
|noname|   |GTR+FO+G4m|   ||
[00:00:00] Reading alignment from file: data/rbcL_ITS2_alignment_resolved.fasta
Failed to load as IPHYLIP: Unable to parse PHYLIP file: data/rbcL_ITS2_alignment_resolved.fasta
 (LIBPLL-231): Invalid number of sequences in header
Failed to load as PHYLIP: Unable to parse PHYLIP file: data/rbcL_ITS2_alignment_resolved.fasta
 (LIBPLL-231): Invalid number of sequences in header
[00:00:00] Loaded alignment with 110 taxa and 1756 sites
[00:00:00] Extracting partitions...
[00:00:00] Checking the alignment...

WARNING: Fully undetermined columns found: 82

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed)
NOTE: was saved to: /mnt/c/Dados/ITV/PIMBA/plwb/test/model/model_eval.raxml.reduced.phy
[00:00:00] Compressing alignment patterns...

Alignment comprises 1 partitions and 1181 patterns

Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 1674 / 1181
Gaps: 34.86 %
Invariant sites: 41.04 %


NOTE: Binary MSA file created: test/model/model_eval.raxml.rba

Recommended threads (response/balanced/throughput): 8 / 5 / 1

Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s)

[00:00:00] Generating a RANDOM starting tree, seed: 1783016762
[00:00:00] Loading user starting tree(s) from: data/APG4_PFC_equal.resolved.newick
Loaded user starting tree with 110 taxa from: data/APG4_PFC_equal.resolved.newick
Parallel reduction/worker buffer size: 1 KB  / 0 KB


Initial model parameters:
   Partition: noname
   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 1.000000 (ML),  weights&rates: (0.250000,0.136954) (0.250000,0.476752) (0.250000,1.000000) (0.250000,2.386294)
   Base frequencies (ML): 0.250000 0.250000 0.250000 0.250000
   Substitution rates (ML): 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000

[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 296 / 4736

thread# part#   start   length  weight
0       0       888     293     4688

1       0       592     296     4736

2       0       296     296     4736

3       0       0       296     4736

[00:00:00] Data distribution: max. searches per worker: 1

BARRIER time: 0.034399 ms

Evaluating 1 trees

Segmentation fault

[Oleksiy Kozlov]

Hi Renato,

thanks for reporting! Could you please send/post your input files?

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[Renato Oliveira]

Hi, Kozlov!

Sure!

I also rerun with other files and got the same error:

/mnt/c/Dados/ITV/PIMBA/plwb$ /mnt/c/Dados/softwares/raxml-ng/raxml-ng --evaluate --msa data/rbcL_ITS2_alignment_resolved.fasta --tree data/APG4_new.newick --model GTR+G --prefix test/model/model_eval --threads 4 --log debug

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: Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz, 2 cores, 12 GB RAM

RAxML-NG was called at 30-May-2023 09:53:05 as follows:

/mnt/c/Dados/softwares/raxml-ng/raxml-ng --evaluate --msa data/rbcL_ITS2_alignment_resolved.fasta --tree data/APG4_new.newick --model GTR+G --prefix test/model/model_eval --threads 4 --log debug

Analysis options:
  run mode: Evaluate tree likelihood
  start tree(s): user

  random seed: 1685451185

NOTE: Binary MSA file already exists: test/model/model_eval.raxml.rba

Recommended threads (response/balanced/throughput): 8 / 5 / 1

Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s)

[00:00:00] Generating a RANDOM starting tree, seed: 1098548396

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


Initial model parameters:
   Partition: noname
   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 1.000000 (ML),  weights&rates: (0.250000,0.136954) (0.250000,0.476752) (0.250000,1.000000) (0.250000,2.386294)
   Base frequencies (ML): 0.250000 0.250000 0.250000 0.250000
   Substitution rates (ML): 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000

[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 296 / 4736

thread# part#   start   length  weight
0       0       888     293     4688

1       0       592     296     4736

2       0       296     296     4736

3       0       0       296     4736

[00:00:00] Data distribution: max. searches per worker: 1

BARRIER time: 0.000295 ms

Evaluating 1 trees

Segmentation fault

Thanks in advance!

[Oleksiy Kozlov]

Hi Renato,

sorry for late response, I cannot reproduce this error, which OS and which raxml-ng binary are you
using?

If on Linux, could you please try with the static binary:

https://github.com/amkozlov/raxml-ng/releases/download/1.2.0/raxml-ng_v1.2.0_linux_x86_64.zip

Best,
Oleksiy

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