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

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

@@ -8,14 +8,14 @@ Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!
 
 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:
+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: 1755385698
+  random seed: 1755531114
   tip-inner: OFF
   pattern compression: ON
   per-rate scalers: OFF
@@ -63,101 +63,103 @@ Parallel reduction/worker buffer size: 1 KB  / 0 KB
 
 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 -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 -662.791501] 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 -662.791498] 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] [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 #5, logLikelihood: -662.791471
+[00:00:00] [worker #0] ML tree search #1, logLikelihood: -662.791470
 
-[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 -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 -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 -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: -662.791471
+[00:00:00] [worker #0] ML tree search #9, logLikelihood: -662.791468
 
-[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] [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 -1004.317937] 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 -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] [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)
@@ -165,61 +167,60 @@ Starting ML tree search with 20 distinct starting trees
 
 [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 -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 -1004.325322] 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 -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 -1004.322428] 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 -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 #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 
+   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: -662.791469
+Final LogLikelihood: -662.791468
 
-AIC score: 1385.582939 / AICc score: 1391.487701 / BIC score: 1500.976102
+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!
@@ -231,9 +232,9 @@ Optimized model saved to: /home/runner/work/partis/partis/test/ref-results/parti
 
 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
+Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:54
 
-Elapsed time: 0.474 seconds
+Elapsed time: 0.438 seconds
 
 
 RAxML-NG v. 1.2.1 released on 22.12.2023 by The Exelixis Lab.
@@ -244,14 +245,14 @@ Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!
 
 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:
+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: 1755385698
+  random seed: 1755531114
   tip-inner: ON
   pattern compression: OFF
   per-rate scalers: OFF
@@ -293,153 +294,153 @@ Parallel reduction/worker buffer size: 1 KB  / 0 KB
 
 Starting ML tree search with 20 distinct starting trees
 
-[00:00:00] Tree #1, initial LogLikelihood: -1045.659744
+[00:00:00] Tree #1, initial LogLikelihood: -1045.799389
 
-[00:00:00 -1045.659744] Initial branch length optimization
-[00:00:00 -738.752348] Model parameter optimization (eps = 10.000000)
+[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: -725.000046
+[00:00:00] Tree #1, final logLikelihood: -721.513060
 
-[00:00:00] Tree #2, initial LogLikelihood: -1046.886052
+[00:00:00] Tree #2, initial LogLikelihood: -1042.991071
 
-[00:00:00 -1046.886052] Initial branch length optimization
-[00:00:00 -738.757373] Model parameter optimization (eps = 10.000000)
+[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: -725.000021
+[00:00:00] Tree #2, final logLikelihood: -724.999913
 
-[00:00:00] Tree #3, initial LogLikelihood: -1042.987303
+[00:00:00] Tree #3, initial LogLikelihood: -1044.315152
 
-[00:00:00 -1042.987303] Initial branch length optimization
-[00:00:00 -738.758082] Model parameter optimization (eps = 10.000000)
+[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: -721.511501
+[00:00:00] Tree #3, final logLikelihood: -725.000038
 
-[00:00:00] Tree #4, initial LogLikelihood: -1040.663132
+[00:00:00] Tree #4, initial LogLikelihood: -1046.884527
 
-[00:00:00 -1040.663132] Initial branch length optimization
-[00:00:00 -725.744207] Model parameter optimization (eps = 10.000000)
+[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: -714.338568
+[00:00:00] Tree #4, final logLikelihood: -724.999994
 
-[00:00:00] Tree #5, initial LogLikelihood: -1044.242985
+[00:00:00] Tree #5, initial LogLikelihood: -1046.752720
 
-[00:00:00 -1044.242985] Initial branch length optimization
-[00:00:00 -738.762719] Model parameter optimization (eps = 10.000000)
+[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: -725.000032
+[00:00:00] Tree #5, final logLikelihood: -724.999992
 
-[00:00:00] Tree #6, initial LogLikelihood: -1030.578002
+[00:00:00] Tree #6, initial LogLikelihood: -1045.789923
 
-[00:00:00 -1030.578002] Initial branch length optimization
-[00:00:00 -720.999971] Model parameter optimization (eps = 10.000000)
+[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: -706.156329
+[00:00:00] Tree #6, final logLikelihood: -720.053445
 
-[00:00:00] Tree #7, initial LogLikelihood: -1040.620761
+[00:00:00] Tree #7, initial LogLikelihood: -1040.657875
 
-[00:00:00 -1040.620761] Initial branch length optimization
-[00:00:00 -725.746446] Model parameter optimization (eps = 10.000000)
+[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: -714.021094
+[00:00:00] Tree #7, final logLikelihood: -714.338581
 
-[00:00:00] Tree #8, initial LogLikelihood: -1045.340747
+[00:00:00] Tree #8, initial LogLikelihood: -1046.739192
 
-[00:00:00 -1045.340747] Initial branch length optimization
-[00:00:00 -734.508881] Model parameter optimization (eps = 10.000000)
+[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: -721.148652
+[00:00:00] Tree #8, final logLikelihood: -725.000026
 
-[00:00:00] Tree #9, initial LogLikelihood: -1046.979195
+[00:00:00] Tree #9, initial LogLikelihood: -1037.579663
 
-[00:00:00 -1046.979195] Initial branch length optimization
-[00:00:00 -738.760469] Model parameter optimization (eps = 10.000000)
+[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: -725.000035
+[00:00:00] Tree #9, final logLikelihood: -714.338579
 
-[00:00:00] Tree #10, initial LogLikelihood: -1045.773389
+[00:00:00] Tree #10, initial LogLikelihood: -1046.872839
 
-[00:00:00 -1045.773389] Initial branch length optimization
-[00:00:00 -738.762327] Model parameter optimization (eps = 10.000000)
+[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: -724.999796
+[00:00:00] Tree #10, final logLikelihood: -725.000023
 
-[00:00:00] Tree #11, initial LogLikelihood: -1004.317870
+[00:00:00] Tree #11, initial LogLikelihood: -1004.325435
 
-[00:00:00 -1004.317870] Initial branch length optimization
-[00:00:00 -668.056483] Model parameter optimization (eps = 10.000000)
+[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: -662.853098
+[00:00:00] Tree #11, final logLikelihood: -662.851646
 
-[00:00:00] Tree #12, initial LogLikelihood: -1004.319632
+[00:00:00] Tree #12, initial LogLikelihood: -1004.326377
 
-[00:00:00 -1004.319632] Initial branch length optimization
-[00:00:00 -668.056544] Model parameter optimization (eps = 10.000000)
+[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: -662.853087
+[00:00:00] Tree #12, final logLikelihood: -662.852089
 
-[00:00:00] Tree #13, initial LogLikelihood: -1004.317937
+[00:00:00] Tree #13, initial LogLikelihood: -1004.325143
 
-[00:00:00 -1004.317937] Initial branch length optimization
-[00:00:00 -668.056736] Model parameter optimization (eps = 10.000000)
+[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: -662.852930
+[00:00:00] Tree #13, final logLikelihood: -662.852619
 
-[00:00:00] Tree #14, initial LogLikelihood: -1004.320321
+[00:00:00] Tree #14, initial LogLikelihood: -1004.317937
 
-[00:00:00 -1004.320321] Initial branch length optimization
-[00:00:00 -668.056272] Model parameter optimization (eps = 10.000000)
+[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: -662.853214
+[00:00:00] Tree #14, final logLikelihood: -662.852662
 
-[00:00:00] Tree #15, initial LogLikelihood: -1004.319559
+[00:00:00] Tree #15, initial LogLikelihood: -1004.317858
 
-[00:00:00 -1004.319559] Initial branch length optimization
-[00:00:00 -668.056446] Model parameter optimization (eps = 10.000000)
+[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: -662.853134
+[00:00:00] Tree #15, final logLikelihood: -662.852672
 
-[00:00:00] Tree #16, initial LogLikelihood: -1004.326398
+[00:00:00] Tree #16, initial LogLikelihood: -1004.319570
 
-[00:00:00 -1004.326398] Initial branch length optimization
-[00:00:00 -668.058705] Model parameter optimization (eps = 10.000000)
+[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: -662.852320
+[00:00:00] Tree #16, final logLikelihood: -662.852976
 
-[00:00:00] Tree #17, initial LogLikelihood: -1004.325322
+[00:00:00] Tree #17, initial LogLikelihood: -1004.322276
 
-[00:00:00 -1004.325322] Initial branch length optimization
-[00:00:00 -668.056408] Model parameter optimization (eps = 10.000000)
+[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: -662.853188
+[00:00:00] Tree #17, final logLikelihood: -662.853119
 
-[00:00:00] Tree #18, initial LogLikelihood: -1004.328189
+[00:00:00] Tree #18, initial LogLikelihood: -1004.326038
 
-[00:00:00 -1004.328189] Initial branch length optimization
-[00:00:00 -668.057815] Model parameter optimization (eps = 10.000000)
+[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: -662.852694
+[00:00:00] Tree #18, final logLikelihood: -662.853175
 
-[00:00:00] Tree #19, initial LogLikelihood: -1004.322428
+[00:00:00] Tree #19, initial LogLikelihood: -1004.319547
 
-[00:00:00 -1004.322428] Initial branch length optimization
-[00:00:00 -668.058423] Model parameter optimization (eps = 10.000000)
+[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: -662.852359
+[00:00:00] Tree #19, final logLikelihood: -662.853237
 
-[00:00:00] Tree #20, initial LogLikelihood: -1004.319412
+[00:00:00] Tree #20, initial LogLikelihood: -1004.326486
 
-[00:00:00 -1004.319412] Initial branch length optimization
-[00:00:00 -668.056741] Model parameter optimization (eps = 10.000000)
+[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: -662.852953
+[00:00:00] Tree #20, final logLikelihood: -662.852624
 
 
 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 
+   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
@@ -447,7 +448,7 @@ Node-labeled tree saved to: /home/runner/work/partis/partis/test/ref-results/par
 
 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
+Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:55
 
-Elapsed time: 0.371 seconds
+Elapsed time: 0.427 seconds
 

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

@@ -1 +1 @@
-((((((91796617a0:0.000001,XnaiveX:0.000001)Node1:0.000001,31e052ee14:0.000001)Node2:0.000001,97366cf0d8:0.002730)Node3:0.000001,13de8675ec:0.000001)Node4:0.000001,4233d708fe:0.000001)Node5:0.000001,33aaa62e12:0.000001,20a0129b57:0.002730)Node6;
+((((((97366cf0d8:0.002730,20a0129b57:0.002730)Node1:0.000001,4233d708fe:0.000001)Node2:0.000001,31e052ee14:0.000001)Node3:0.000001,13de8675ec:0.000001)Node4:0.000001,XnaiveX:0.000001)Node5:0.000001,91796617a0:0.000001,33aaa62e12:0.000001)Node6;

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

@@ -1 +1 @@
-(20a0129b57:0.002731,(((((91796617a0:0.000001,31e052ee14:0.000001):0.000001,4233d708fe:0.000001):0.000001,XnaiveX:0.000001):0.000001,13de8675ec:0.000001):0.000001,33aaa62e12:0.000001):0.000001,97366cf0d8:0.002730);
+((33aaa62e12:0.000001,XnaiveX:0.000001):0.000001,(31e052ee14:0.000001,(4233d708fe:0.000001,(91796617a0:0.000001,13de8675ec:0.000001):0.000001):0.000001):0.000001,(97366cf0d8:0.002730,20a0129b57:0.002731):0.000001);

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

@@ -1 +1 @@
-(20a0129b57:0.002731,91796617a0:0.000001,31e052ee14:0.000001,4233d708fe:0.000001,XnaiveX:0.000001,13de8675ec:0.000001,33aaa62e12:0.000001,97366cf0d8:0.002730);
+(XnaiveX:0.000001,31e052ee14:0.000001,4233d708fe:0.000001,91796617a0:0.000001,13de8675ec:0.000001,97366cf0d8:0.002730,20a0129b57:0.002731,33aaa62e12:0.000001);