partis-bcr 1.0.8__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.whl

test/ref-results/partition-new-simu/raxml/iclust-0/log

@@ -0,0 +1,454 @@
+run /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/run.sh
+
+RAxML-NG v. 1.2.1 released on 22.12.2023 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: AMD EPYC 7763 64-Core Processor, 2 cores, 15 GB RAM
+
+RAxML-NG was called at 18-Aug-2025 15:31:54 as follows:
+
+/home/runner/work/partis/partis/bin/raxml-ng-linux --model GTR+G --msa /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa --msa-format FASTA
+
+Analysis options:
+  run mode: ML tree search
+  start tree(s): random (10) + parsimony (10)
+  random seed: 1755531114
+  tip-inner: OFF
+  pattern compression: ON
+  per-rate scalers: OFF
+  site repeats: ON
+  logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000
+  fast spr radius: AUTO
+  spr subtree cutoff: 1.000000
+  fast CLV updates: ON
+  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
+  SIMD kernels: AVX2
+  parallelization: coarse-grained (auto), PTHREADS (auto)
+
+[00:00:00] Reading alignment from file: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa
+[00:00:00] Loaded alignment with 12 taxa and 346 sites
+
+WARNING: Sequences XnaiveX and 822801f8ab are exactly identical!
+WARNING: Sequences XnaiveX and d024e5cab0 are exactly identical!
+WARNING: Sequences 648902c3e5 and 8024ed1a22 are exactly identical!
+WARNING: Sequences 648902c3e5 and f47122f1f5 are exactly identical!
+WARNING: Duplicate sequences found: 4
+
+NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
+NOTE: was saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.reduced.phy
+
+Alignment comprises 1 partitions and 28 patterns
+
+Partition 0: noname
+Model: GTR+FO+G4m
+Alignment sites / patterns: 346 / 28
+Gaps: 0.00 %
+Invariant sites: 91.91 %
+
+
+NOTE: Binary MSA file created: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.rba
+
+Parallelization scheme autoconfig: 2 worker(s) x 1 thread(s)
+
+[00:00:00] Generating 10 random starting tree(s) with 12 taxa
+[00:00:00] Generating 10 parsimony starting tree(s) with 12 taxa
+Parallel parsimony with 2 threads
+Parallel reduction/worker buffer size: 1 KB  / 0 KB
+
+[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 28 / 448
+[00:00:00] Data distribution: max. searches per worker: 10
+
+Starting ML tree search with 20 distinct starting trees
+
+[00:00:00 -1045.799389] Initial branch length optimization
+[00:00:00 -738.757363] Model parameter optimization (eps = 10.000000)
+[00:00:00 -721.513060] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -667.283457] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -667.283124] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -667.283124] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791501] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791498] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791473] SLOW spr round 1 (radius: 5)
+[00:00:00] [worker #1] ML tree search #2, logLikelihood: -662.791470
+[00:00:00 -662.791472] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791472] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #1, logLikelihood: -662.791470
+
+[00:00:00 -1044.315152] Initial branch length optimization
+[00:00:00 -738.757558] Model parameter optimization (eps = 10.000000)
+[00:00:00 -725.000038] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -667.309711] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -667.309597] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -667.309597] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791503] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791503] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791472] SLOW spr round 1 (radius: 5)
+[00:00:00] [worker #1] ML tree search #4, logLikelihood: -662.791471
+[00:00:00 -662.791471] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791471] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #3, logLikelihood: -662.791470
+
+[00:00:00 -1046.752720] Initial branch length optimization
+[00:00:00 -738.764057] Model parameter optimization (eps = 10.000000)
+[00:00:00 -724.999992] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -681.955819] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -681.955311] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -681.955311] Model parameter optimization (eps = 3.000000)
+[00:00:00 -680.508761] FAST spr round 1 (radius: 5)
+[00:00:00 -665.976887] FAST spr round 2 (radius: 5)
+[00:00:00 -665.976834] Model parameter optimization (eps = 1.000000)
+[00:00:00] [worker #1] ML tree search #6, logLikelihood: -662.791474
+[00:00:00 -662.791497] SLOW spr round 1 (radius: 5)
+[00:00:00 -662.791497] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791497] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #5, logLikelihood: -662.791474
+
+[00:00:00 -1040.657875] Initial branch length optimization
+[00:00:00 -725.750218] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #8, logLikelihood: -662.791470
+[00:00:00 -714.338581] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -667.020376] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -667.019890] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -667.019890] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791506] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791506] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791472] SLOW spr round 1 (radius: 5)
+[00:00:00 -662.791472] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791472] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #7, logLikelihood: -662.791471
+
+[00:00:00 -1037.579663] Initial branch length optimization
+[00:00:00 -725.744211] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #10, logLikelihood: -662.791471
+[00:00:00 -714.338579] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -674.484047] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -673.604711] SPR radius for FAST iterations: 10 (autodetect)
+[00:00:00 -673.604711] Model parameter optimization (eps = 3.000000)
+[00:00:00 -672.171392] FAST spr round 1 (radius: 10)
+[00:00:00 -663.832295] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791472] SLOW spr round 1 (radius: 5)
+[00:00:00 -662.791471] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791471] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #9, logLikelihood: -662.791468
+
+[00:00:00] [worker #1] ML tree search #12, logLikelihood: -662.791470
+[00:00:00 -1004.325435] Initial branch length optimization
+[00:00:00 -668.062208] Model parameter optimization (eps = 10.000000)
+[00:00:00 -662.851646] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -662.851644] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.851644] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791487] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791487] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791471] SLOW spr round 1 (radius: 5)
+[00:00:00 -662.791471] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791471] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #11, logLikelihood: -662.791469
+
+[00:00:00 -1004.325143] Initial branch length optimization
+[00:00:00 -668.057580] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #14, logLikelihood: -662.791470
+[00:00:00 -662.852619] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -662.852616] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.852616] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791488] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791488] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791471] SLOW spr round 1 (radius: 5)
+[00:00:00 -662.791471] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791471] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #13, logLikelihood: -662.791470
+
+[00:00:00 -1004.317858] Initial branch length optimization
+[00:00:00 -668.057079] Model parameter optimization (eps = 10.000000)
+[00:00:00 -662.852672] AUTODETECT spr round 1 (radius: 5)
+[00:00:00] [worker #1] ML tree search #16, logLikelihood: -662.791470
+[00:00:00 -662.852668] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.852668] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791489] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791489] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791472] SLOW spr round 1 (radius: 5)
+[00:00:00 -662.791471] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791471] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #15, logLikelihood: -662.791469
+
+[00:00:00 -1004.322276] Initial branch length optimization
+[00:00:00 -668.056467] Model parameter optimization (eps = 10.000000)
+[00:00:00 -662.853119] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -662.853118] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.853118] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791488] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791488] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791472] SLOW spr round 1 (radius: 5)
+[00:00:00 -662.791472] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791472] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #17, logLikelihood: -662.791470
+
+[00:00:00 -1004.319547] Initial branch length optimization
+[00:00:00 -668.056307] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #18, logLikelihood: -662.791470
+[00:00:00 -662.853237] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -662.853234] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.853234] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791489] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791489] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791472] SLOW spr round 1 (radius: 5)
+[00:00:00 -662.791472] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791472] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #19, logLikelihood: -662.791470
+
+[00:00:00] [worker #1] ML tree search #20, logLikelihood: -662.791470
+
+Optimized model parameters:
+
+   Partition 0: noname
+   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 99.859525 (ML),  weights&rates: (0.250000,0.875821) (0.250000,0.964712) (0.250000,1.029568) (0.250000,1.129899) 
+   Base frequencies (ML): 0.218404 0.257148 0.305098 0.219350 
+   Substitution rates (ML): 0.977189 0.983302 0.461388 0.701156 0.796913 1.000000 
+
+
+Final LogLikelihood: -662.791468
+
+AIC score: 1385.582937 / AICc score: 1391.487699 / BIC score: 1500.976100
+Free parameters (model + branch lengths): 30
+
+WARNING: Best ML tree contains 6 near-zero branches!
+
+Best ML tree with collapsed near-zero branches saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed
+Best ML tree saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree
+All ML trees saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees
+Optimized model saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel
+
+Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log
+
+Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:54
+
+Elapsed time: 0.438 seconds
+
+
+RAxML-NG v. 1.2.1 released on 22.12.2023 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: AMD EPYC 7763 64-Core Processor, 2 cores, 15 GB RAM
+
+RAxML-NG was called at 18-Aug-2025 15:31:54 as follows:
+
+/home/runner/work/partis/partis/bin/raxml-ng-linux --model GTR+G --msa /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa --msa-format FASTA --ancestral --tree /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree
+
+Analysis options:
+  run mode: Ancestral state reconstruction
+  start tree(s): user
+  random seed: 1755531114
+  tip-inner: ON
+  pattern compression: OFF
+  per-rate scalers: OFF
+  site repeats: OFF
+  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 (auto)
+
+[00:00:00] Reading alignment from file: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa
+[00:00:00] Loaded alignment with 12 taxa and 346 sites
+
+WARNING: Sequences XnaiveX and 822801f8ab are exactly identical!
+WARNING: Sequences XnaiveX and d024e5cab0 are exactly identical!
+WARNING: Sequences 648902c3e5 and 8024ed1a22 are exactly identical!
+WARNING: Sequences 648902c3e5 and f47122f1f5 are exactly identical!
+WARNING: Duplicate sequences found: 4
+
+NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
+NOTE: was saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.reduced.phy
+
+Alignment comprises 1 partitions and 346 sites
+
+Partition 0: noname
+Model: GTR+FO+G4m
+Alignment sites: 346
+Gaps: 0.00 %
+Invariant sites: 91.91 %
+
+
+NOTE: Binary MSA file already exists: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.rba
+
+Parallelization scheme autoconfig: 1 worker(s) x 2 thread(s)
+
+Parallel reduction/worker buffer size: 1 KB  / 0 KB
+
+[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 173 / 2768
+[00:00:00] Data distribution: max. searches per worker: 20
+
+Starting ML tree search with 20 distinct starting trees
+
+[00:00:00] Tree #1, initial LogLikelihood: -1045.799389
+
+[00:00:00 -1045.799389] Initial branch length optimization
+[00:00:00 -738.757363] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #1, final logLikelihood: -721.513060
+
+[00:00:00] Tree #2, initial LogLikelihood: -1042.991071
+
+[00:00:00 -1042.991071] Initial branch length optimization
+[00:00:00 -738.756586] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #2, final logLikelihood: -724.999913
+
+[00:00:00] Tree #3, initial LogLikelihood: -1044.315152
+
+[00:00:00 -1044.315152] Initial branch length optimization
+[00:00:00 -738.757558] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #3, final logLikelihood: -725.000038
+
+[00:00:00] Tree #4, initial LogLikelihood: -1046.884527
+
+[00:00:00 -1046.884527] Initial branch length optimization
+[00:00:00 -738.762782] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #4, final logLikelihood: -724.999994
+
+[00:00:00] Tree #5, initial LogLikelihood: -1046.752720
+
+[00:00:00 -1046.752720] Initial branch length optimization
+[00:00:00 -738.764057] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #5, final logLikelihood: -724.999992
+
+[00:00:00] Tree #6, initial LogLikelihood: -1045.789923
+
+[00:00:00 -1045.789923] Initial branch length optimization
+[00:00:00 -734.508910] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #6, final logLikelihood: -720.053445
+
+[00:00:00] Tree #7, initial LogLikelihood: -1040.657875
+
+[00:00:00 -1040.657875] Initial branch length optimization
+[00:00:00 -725.750218] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #7, final logLikelihood: -714.338581
+
+[00:00:00] Tree #8, initial LogLikelihood: -1046.739192
+
+[00:00:00 -1046.739192] Initial branch length optimization
+[00:00:00 -738.761728] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #8, final logLikelihood: -725.000026
+
+[00:00:00] Tree #9, initial LogLikelihood: -1037.579663
+
+[00:00:00 -1037.579663] Initial branch length optimization
+[00:00:00 -725.744211] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #9, final logLikelihood: -714.338579
+
+[00:00:00] Tree #10, initial LogLikelihood: -1046.872839
+
+[00:00:00 -1046.872839] Initial branch length optimization
+[00:00:00 -738.760423] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #10, final logLikelihood: -725.000023
+
+[00:00:00] Tree #11, initial LogLikelihood: -1004.325435
+
+[00:00:00 -1004.325435] Initial branch length optimization
+[00:00:00 -668.062208] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #11, final logLikelihood: -662.851646
+
+[00:00:00] Tree #12, initial LogLikelihood: -1004.326377
+
+[00:00:00 -1004.326377] Initial branch length optimization
+[00:00:00 -668.059976] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #12, final logLikelihood: -662.852089
+
+[00:00:00] Tree #13, initial LogLikelihood: -1004.325143
+
+[00:00:00 -1004.325143] Initial branch length optimization
+[00:00:00 -668.057580] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #13, final logLikelihood: -662.852619
+
+[00:00:00] Tree #14, initial LogLikelihood: -1004.317937
+
+[00:00:00 -1004.317937] Initial branch length optimization
+[00:00:00 -668.057282] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #14, final logLikelihood: -662.852662
+
+[00:00:00] Tree #15, initial LogLikelihood: -1004.317858
+
+[00:00:00 -1004.317858] Initial branch length optimization
+[00:00:00 -668.057079] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #15, final logLikelihood: -662.852672
+
+[00:00:00] Tree #16, initial LogLikelihood: -1004.319570
+
+[00:00:00 -1004.319570] Initial branch length optimization
+[00:00:00 -668.056689] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #16, final logLikelihood: -662.852976
+
+[00:00:00] Tree #17, initial LogLikelihood: -1004.322276
+
+[00:00:00 -1004.322276] Initial branch length optimization
+[00:00:00 -668.056467] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #17, final logLikelihood: -662.853119
+
+[00:00:00] Tree #18, initial LogLikelihood: -1004.326038
+
+[00:00:00 -1004.326038] Initial branch length optimization
+[00:00:00 -668.056343] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #18, final logLikelihood: -662.853175
+
+[00:00:00] Tree #19, initial LogLikelihood: -1004.319547
+
+[00:00:00 -1004.319547] Initial branch length optimization
+[00:00:00 -668.056307] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #19, final logLikelihood: -662.853237
+
+[00:00:00] Tree #20, initial LogLikelihood: -1004.326486
+
+[00:00:00 -1004.326486] Initial branch length optimization
+[00:00:00 -668.057933] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #20, final logLikelihood: -662.852624
+
+
+Optimized model parameters:
+
+   Partition 0: noname
+   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 99.862237 (ML),  weights&rates: (0.250000,0.875822) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897) 
+   Base frequencies (ML): 0.219082 0.256999 0.304238 0.219681 
+   Substitution rates (ML): 0.897660 0.970520 0.394048 0.762800 0.745857 1.000000 
+
+Marginal ancestral probabilities saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs
+Reconstructed ancestral sequences saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates
+Node-labeled tree saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree
+
+Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log
+
+Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:55
+
+Elapsed time: 0.427 seconds
+

test/ref-results/partition-new-simu/raxml/iclust-0/run.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+/home/runner/work/partis/partis/bin/raxml-ng-linux --model GTR+G --msa /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa --msa-format FASTA
+/home/runner/work/partis/partis/bin/raxml-ng-linux --model GTR+G --msa /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa --msa-format FASTA --ancestral --tree /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree

test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa

@@ -0,0 +1,16 @@
+>XnaiveX
+CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>13de8675ec
+CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>20a0129b57
+CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTAGTCACCGTCTCCTCAG
+>31e052ee14
+CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>33aaa62e12
+CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>4233d708fe
+CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>91796617a0
+CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
+>97366cf0d8
+CAGGTTCAGCTGGTTCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG