
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 10:22:20 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_all/pargenes-hpc-debug/parse_run/results/msa4_fasta/msa4_fasta.raxml.rba --model JC --prefix /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc-debug/mlsearch_run/results/msa4_fasta/multiple_runs/5/msa4_fasta --threads 1 --tree pars{1} --seed 6

Analysis options:
  run mode: ML tree search
  start tree(s): parsimony (1)
  random seed: 6
  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 (JC) 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_all/pargenes-hpc-debug/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: JC
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 / 152

Starting ML tree search with 1 distinct starting trees

[00:00:00 -164.872180] Initial branch length optimization
[00:00:00 -135.273247] Model parameter optimization (eps = 10.000000)
[00:00:00 -135.259381] SPR radius for FAST iterations: 5 (autodetect)
[00:00:00 -135.259381] Model parameter optimization (eps = 3.000000)
[00:00:00 -135.237469] FAST spr round 1 (radius: 5)
[00:00:00 -135.157939] Model parameter optimization (eps = 1.000000)
[00:00:00 -135.126260] SLOW spr round 1 (radius: 5)
[00:00:00 -135.091153] Model parameter optimization (eps = 0.100000)

[00:00:00] ML tree search #1, logLikelihood: -135.079025


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: NONE
   Base frequencies (model): 0.250000 0.250000 0.250000 0.250000 
   Substitution rates (model): 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 


Final LogLikelihood: -135.079025

AIC score: 280.158051 / AICc score: 281.621465 / BIC score: 289.408789
Free parameters (model + branch lengths): 5

Best ML tree saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc-debug/mlsearch_run/results/msa4_fasta/multiple_runs/5/msa4_fasta.raxml.bestTree
Optimized model saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc-debug/mlsearch_run/results/msa4_fasta/multiple_runs/5/msa4_fasta.raxml.bestModel

Execution log saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc-debug/mlsearch_run/results/msa4_fasta/multiple_runs/5/msa4_fasta.raxml.log

Analysis started: 25-Dec-2020 10:22:20 / finished: 25-Dec-2020 10:22:20

Elapsed time: 0.010 seconds

