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

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

@@ -0,0 +1,453 @@
+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 16-Aug-2025 23:08:18 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: 1755385698
+  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 -1045.659744] Initial branch length optimization
+[00:00:00 -738.752348] Model parameter optimization (eps = 10.000000)
+[00:00:00 -725.000046] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -667.311161] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -667.310248] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -667.310248] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791501] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791501] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791471] SLOW spr round 1 (radius: 5)
+[00:00:00] [worker #1] ML tree search #2, 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 #1, logLikelihood: -662.791470
+
+[00:00:00 -1042.987303] Initial branch length optimization
+[00:00:00 -738.758082] Model parameter optimization (eps = 10.000000)
+[00:00:00 -721.511501] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -667.284817] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -667.283378] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -667.283378] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791500] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791499] Model parameter optimization (eps = 1.000000)
+[00:00:00 -662.791473] SLOW spr round 1 (radius: 5)
+[00:00:00 -662.791473] SLOW spr round 2 (radius: 10)
+[00:00:00 -662.791473] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #3, logLikelihood: -662.791472
+
+[00:00:00 -1044.242985] Initial branch length optimization
+[00:00:00] [worker #1] ML tree search #4, logLikelihood: -662.791471
+[00:00:00 -738.762719] Model parameter optimization (eps = 10.000000)
+[00:00:00 -725.000032] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -667.308516] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -667.308409] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -667.308409] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791502] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791502] 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 #5, logLikelihood: -662.791471
+
+[00:00:00 -1040.620761] Initial branch length optimization
+[00:00:00 -725.746446] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #6, logLikelihood: -662.791471
+[00:00:00 -714.021094] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -666.888499] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -666.888395] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -666.888395] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791501] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791501] 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 -1046.979195] Initial branch length optimization
+[00:00:00 -738.760469] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #8, logLikelihood: -662.791470
+[00:00:00 -725.000035] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -667.309427] AUTODETECT spr round 2 (radius: 10)
+[00:00:00 -667.309274] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -667.309274] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791502] FAST spr round 1 (radius: 5)
+[00:00:00 -662.791502] 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 #9, logLikelihood: -662.791471
+
+[00:00:00 -1004.317870] Initial branch length optimization
+[00:00:00 -668.056483] Model parameter optimization (eps = 10.000000)
+[00:00:00 -662.853098] AUTODETECT spr round 1 (radius: 5)
+[00:00:00] [worker #1] ML tree search #10, logLikelihood: -662.791472
+[00:00:00 -662.853095] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.853095] 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 #11, logLikelihood: -662.791469
+
+[00:00:00 -1004.317937] Initial branch length optimization
+[00:00:00 -668.056736] Model parameter optimization (eps = 10.000000)
+[00:00:00 -662.852930] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -662.852926] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.852926] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791488] FAST spr round 1 (radius: 5)
+[00:00:00] [worker #1] ML tree search #12, logLikelihood: -662.791470
+[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 -1004.319559] Initial branch length optimization
+[00:00:00 -668.056446] Model parameter optimization (eps = 10.000000)
+[00:00:00 -662.853134] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -662.853130] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.853130] Model parameter optimization (eps = 3.000000)
+[00:00:00] [worker #1] ML tree search #14, logLikelihood: -662.791471
+[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 #15, logLikelihood: -662.791469
+
+[00:00:00 -1004.325322] Initial branch length optimization
+[00:00:00 -668.056408] Model parameter optimization (eps = 10.000000)
+[00:00:00 -662.853188] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -662.853185] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.853185] Model parameter optimization (eps = 3.000000)
+[00:00:00 -662.791489] FAST spr round 1 (radius: 5)
+[00:00:00] [worker #1] ML tree search #16, logLikelihood: -662.791470
+[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 #17, logLikelihood: -662.791470
+
+[00:00:00 -1004.322428] Initial branch length optimization
+[00:00:00 -668.058423] Model parameter optimization (eps = 10.000000)
+[00:00:00 -662.852359] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -662.852357] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -662.852357] 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 #19, logLikelihood: -662.791470
+
+[00:00:00] [worker #1] ML tree search #18, 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: 99.862254 (ML),  weights&rates: (0.250000,0.875822) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897) 
+   Base frequencies (ML): 0.218410 0.257146 0.305095 0.219349 
+   Substitution rates (ML): 0.976979 0.982855 0.461252 0.700964 0.796581 1.000000 
+
+
+Final LogLikelihood: -662.791469
+
+AIC score: 1385.582939 / AICc score: 1391.487701 / BIC score: 1500.976102
+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: 16-Aug-2025 23:08:18 / finished: 16-Aug-2025 23:08:18
+
+Elapsed time: 0.474 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 16-Aug-2025 23:08:18 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: 1755385698
+  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: -1045.659744
+
+[00:00:00 -1045.659744] Initial branch length optimization
+[00:00:00 -738.752348] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #1, final logLikelihood: -725.000046
+
+[00:00:00] Tree #2, initial LogLikelihood: -1046.886052
+
+[00:00:00 -1046.886052] Initial branch length optimization
+[00:00:00 -738.757373] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #2, final logLikelihood: -725.000021
+
+[00:00:00] Tree #3, initial LogLikelihood: -1042.987303
+
+[00:00:00 -1042.987303] Initial branch length optimization
+[00:00:00 -738.758082] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #3, final logLikelihood: -721.511501
+
+[00:00:00] Tree #4, initial LogLikelihood: -1040.663132
+
+[00:00:00 -1040.663132] Initial branch length optimization
+[00:00:00 -725.744207] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #4, final logLikelihood: -714.338568
+
+[00:00:00] Tree #5, initial LogLikelihood: -1044.242985
+
+[00:00:00 -1044.242985] Initial branch length optimization
+[00:00:00 -738.762719] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #5, final logLikelihood: -725.000032
+
+[00:00:00] Tree #6, initial LogLikelihood: -1030.578002
+
+[00:00:00 -1030.578002] Initial branch length optimization
+[00:00:00 -720.999971] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #6, final logLikelihood: -706.156329
+
+[00:00:00] Tree #7, initial LogLikelihood: -1040.620761
+
+[00:00:00 -1040.620761] Initial branch length optimization
+[00:00:00 -725.746446] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #7, final logLikelihood: -714.021094
+
+[00:00:00] Tree #8, initial LogLikelihood: -1045.340747
+
+[00:00:00 -1045.340747] Initial branch length optimization
+[00:00:00 -734.508881] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #8, final logLikelihood: -721.148652
+
+[00:00:00] Tree #9, initial LogLikelihood: -1046.979195
+
+[00:00:00 -1046.979195] Initial branch length optimization
+[00:00:00 -738.760469] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #9, final logLikelihood: -725.000035
+
+[00:00:00] Tree #10, initial LogLikelihood: -1045.773389
+
+[00:00:00 -1045.773389] Initial branch length optimization
+[00:00:00 -738.762327] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #10, final logLikelihood: -724.999796
+
+[00:00:00] Tree #11, initial LogLikelihood: -1004.317870
+
+[00:00:00 -1004.317870] Initial branch length optimization
+[00:00:00 -668.056483] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #11, final logLikelihood: -662.853098
+
+[00:00:00] Tree #12, initial LogLikelihood: -1004.319632
+
+[00:00:00 -1004.319632] Initial branch length optimization
+[00:00:00 -668.056544] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #12, final logLikelihood: -662.853087
+
+[00:00:00] Tree #13, initial LogLikelihood: -1004.317937
+
+[00:00:00 -1004.317937] Initial branch length optimization
+[00:00:00 -668.056736] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #13, final logLikelihood: -662.852930
+
+[00:00:00] Tree #14, initial LogLikelihood: -1004.320321
+
+[00:00:00 -1004.320321] Initial branch length optimization
+[00:00:00 -668.056272] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #14, final logLikelihood: -662.853214
+
+[00:00:00] Tree #15, initial LogLikelihood: -1004.319559
+
+[00:00:00 -1004.319559] Initial branch length optimization
+[00:00:00 -668.056446] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #15, final logLikelihood: -662.853134
+
+[00:00:00] Tree #16, initial LogLikelihood: -1004.326398
+
+[00:00:00 -1004.326398] Initial branch length optimization
+[00:00:00 -668.058705] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #16, final logLikelihood: -662.852320
+
+[00:00:00] Tree #17, initial LogLikelihood: -1004.325322
+
+[00:00:00 -1004.325322] Initial branch length optimization
+[00:00:00 -668.056408] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #17, final logLikelihood: -662.853188
+
+[00:00:00] Tree #18, initial LogLikelihood: -1004.328189
+
+[00:00:00 -1004.328189] Initial branch length optimization
+[00:00:00 -668.057815] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #18, final logLikelihood: -662.852694
+
+[00:00:00] Tree #19, initial LogLikelihood: -1004.322428
+
+[00:00:00 -1004.322428] Initial branch length optimization
+[00:00:00 -668.058423] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #19, final logLikelihood: -662.852359
+
+[00:00:00] Tree #20, initial LogLikelihood: -1004.319412
+
+[00:00:00 -1004.319412] Initial branch length optimization
+[00:00:00 -668.056741] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #20, final logLikelihood: -662.852953
+
+
+Optimized model parameters:
+
+   Partition 0: noname
+   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 99.862246 (ML),  weights&rates: (0.250000,0.875822) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897) 
+   Base frequencies (ML): 0.219082 0.257002 0.304229 0.219686 
+   Substitution rates (ML): 0.897311 0.970592 0.393839 0.763217 0.745304 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: 16-Aug-2025 23:08:18 / finished: 16-Aug-2025 23:08:19
+
+Elapsed time: 0.371 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