
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 10:13:50 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-hpc-debug/parse_run/results/msa1_fasta/msa1_fasta.raxml.rba --model GTR+G --prefix /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes-hpc-debug/mlsearch_run/results/msa1_fasta/multiple_runs/3/msa1_fasta --threads 1 --tree pars{1} --seed 4

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-hpc-debug/parse_run/results/msa1_fasta/msa1_fasta.raxml.rba
[00:00:00] Alignment comprises 4 taxa, 1 partitions and 39 patterns

Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 47 / 39
Gaps: 31.91 %
Invariant sites: 42.55 %


[00:00:00] Generating 1 parsimony starting tree(s) with 4 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 39 / 624

Starting ML tree search with 1 distinct starting trees

[00:00:00 -172.706129] Initial branch length optimization
[00:00:00 -142.104311] Model parameter optimization (eps = 10.000000)
[00:00:00 -137.181044] SPR radius for FAST iterations: 5 (autodetect)
[00:00:00 -137.181044] Model parameter optimization (eps = 3.000000)
[00:00:00 -137.092550] FAST spr round 1 (radius: 5)
[00:00:00 -137.089701] Model parameter optimization (eps = 1.000000)
[00:00:00 -137.069980] SLOW spr round 1 (radius: 5)
[00:00:00 -137.068267] Model parameter optimization (eps = 0.100000)

[00:00:00] ML tree search #1, logLikelihood: -137.050893


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 99.851905 (ML),  weights&rates: (0.250000,0.875816) (0.250000,0.964711) (0.250000,1.029569) (0.250000,1.129904) 
   Base frequencies (ML): 0.269110 0.222744 0.245198 0.262949 
   Substitution rates (ML): 76.487985 0.001000 4.946023 36.697367 1.186985 1.000000 


Final LogLikelihood: -137.050893

AIC score: 302.101785 / AICc score: 315.226785 / BIC score: 328.003852
Free parameters (model + branch lengths): 14

Best ML tree saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes-hpc-debug/mlsearch_run/results/msa1_fasta/multiple_runs/3/msa1_fasta.raxml.bestTree
Optimized model saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes-hpc-debug/mlsearch_run/results/msa1_fasta/multiple_runs/3/msa1_fasta.raxml.bestModel

Execution log saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_astral/pargenes-hpc-debug/mlsearch_run/results/msa1_fasta/multiple_runs/3/msa1_fasta.raxml.log

Analysis started: 25-Dec-2020 10:13:50 / finished: 25-Dec-2020 10:13:50

Elapsed time: 0.062 seconds

