mpi-scheduler --msa /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc/parse_run/results/msa3_fasta/msa3_fasta.raxml.rba --model JC --prefix /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc/mlsearch_run/results/msa3_fasta/multiple_runs/4/msa3_fasta --threads 1 --tree pars{1} --seed 5 

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 10:13:42 as follows:

mpi-scheduler --msa /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc/parse_run/results/msa3_fasta/msa3_fasta.raxml.rba --model JC --prefix /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc/mlsearch_run/results/msa3_fasta/multiple_runs/4/msa3_fasta --threads 1 --tree pars{1} --seed 5

Analysis options:
  run mode: ML tree search
  start tree(s): parsimony (1)
  random seed: 5
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000
  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/parse_run/results/msa3_fasta/msa3_fasta.raxml.rba
[00:00:00] Alignment comprises 4 taxa, 1 partitions and 39 patterns

Partition 0: noname
Model: JC
Alignment sites / patterns: 47 / 39
Gaps: 31.38 %
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 / 156

Starting ML tree search with 1 distinct starting trees

[00:00:00 -176.177676] Initial branch length optimization
[00:00:00 -149.517855] Model parameter optimization (eps = 10.000000)
[00:00:00 -149.517227] SPR radius for FAST iterations: 5 (autodetect)
[00:00:00 -149.517227] Model parameter optimization (eps = 3.000000)
[00:00:00 -149.516594] FAST spr round 1 (radius: 5)
[00:00:00 -149.515236] Model parameter optimization (eps = 1.000000)
[00:00:00 -149.514518] SLOW spr round 1 (radius: 5)
[00:00:00 -149.513005] Model parameter optimization (eps = 0.100000)

[00:00:00] ML tree search #1, logLikelihood: -149.512204


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: -149.512204

AIC score: 309.024408 / AICc score: 310.487822 / BIC score: 318.275146
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/mlsearch_run/results/msa3_fasta/multiple_runs/4/msa3_fasta.raxml.bestTree
Optimized model saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc/mlsearch_run/results/msa3_fasta/multiple_runs/4/msa3_fasta.raxml.bestModel

Execution log saved to: /opt/conda/conda-bld/pargenes_1608889558035/work/tests/tests_outputs/test_all/pargenes-hpc/mlsearch_run/results/msa3_fasta/multiple_runs/4/msa3_fasta.raxml.log

Analysis started: 25-Dec-2020 10:13:42 / finished: 25-Dec-2020 10:13:42

Elapsed time: 0.014 seconds

