
RAxML-NG v. 0.9.0 released on 20.05.2019 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 25-Dec-2020 10:13:31 as follows:

/opt/conda/conda-bld/pargenes_1608889558035/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/pargenes_src/../pargenes_binaries/raxml-ng --msa /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes/parse_run/results/msa4_fasta/msa4_fasta.raxml.rba --model GTR+G --prefix /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes/mlsearch_run/results/msa4_fasta/multiple_runs/3/msa4_fasta --tree pars{1} --seed 4 --threads 1

Analysis options:
  run mode: ML tree search
  start tree(s): parsimony (1)
  random seed: 4
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: NONE/sequential

WARNING: The model you specified on the command line (GTR+G) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes/parse_run/results/msa4_fasta/msa4_fasta.raxml.rba
[00:00:00] Alignment comprises 4 taxa, 1 partitions and 38 patterns

Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 47 / 38
Gaps: 31.38 %
Invariant sites: 44.68 %


[00:00:00] Generating 1 parsimony starting tree(s) with 4 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 38 / 608

Starting ML tree search with 1 distinct starting trees

[00:00:00 -168.192931] Initial branch length optimization
[00:00:00 -135.294193] Model parameter optimization (eps = 10.000000)
[00:00:00 -132.420153] SPR radius for FAST iterations: 5 (autodetect)
[00:00:00 -132.420153] Model parameter optimization (eps = 3.000000)
[00:00:00 -131.852495] FAST spr round 1 (radius: 5)
[00:00:00 -131.852258] Model parameter optimization (eps = 1.000000)
[00:00:00 -131.698876] SLOW spr round 1 (radius: 5)
[00:00:00 -131.698876] Model parameter optimization (eps = 0.100000)

[00:00:00] ML tree search #1, logLikelihood: -131.622967


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 11.587610 (ML),  weights&rates: (0.250000,0.655159) (0.250000,0.881660) (0.250000,1.069296) (0.250000,1.393884) 
   Base frequencies (ML): 0.272918 0.222465 0.239732 0.264885 
   Substitution rates (ML): 0.001000 23.333552 8.328896 0.096271 72.009010 1.000000 


Final LogLikelihood: -131.622967

AIC score: 291.245934 / AICc score: 304.370934 / BIC score: 317.148000
Free parameters (model + branch lengths): 14

Best ML tree saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes/mlsearch_run/results/msa4_fasta/multiple_runs/3/msa4_fasta.raxml.bestTree
Optimized model saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes/mlsearch_run/results/msa4_fasta/multiple_runs/3/msa4_fasta.raxml.bestModel

Execution log saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes/mlsearch_run/results/msa4_fasta/multiple_runs/3/msa4_fasta.raxml.log

Analysis started: 25-Dec-2020 10:13:31 / finished: 25-Dec-2020 10:13:31

Elapsed time: 0.046 seconds

