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-1/log

@@ -0,0 +1,440 @@
+run /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/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-1/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-1/input-seqs.fa
+[00:00:00] Loaded alignment with 8 taxa and 367 sites
+
+WARNING: Sequences XnaiveX and 13de8675ec are exactly identical!
+WARNING: Sequences XnaiveX and 31e052ee14 are exactly identical!
+WARNING: Sequences XnaiveX and 33aaa62e12 are exactly identical!
+WARNING: Sequences XnaiveX and 4233d708fe are exactly identical!
+WARNING: Sequences XnaiveX and 91796617a0 are exactly identical!
+WARNING: Duplicate sequences found: 5
+
+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-1/input-seqs.fa.raxml.reduced.phy
+
+Alignment comprises 1 partitions and 6 patterns
+
+Partition 0: noname
+Model: GTR+FO+G4m
+Alignment sites / patterns: 367 / 6
+Gaps: 0.00 %
+Invariant sites: 99.46 %
+
+
+NOTE: Binary MSA file created: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/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 8 taxa
+[00:00:00] Generating 10 parsimony starting tree(s) with 8 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 / 6 / 96
+[00:00:00] Data distribution: max. searches per worker: 10
+
+Starting ML tree search with 20 distinct starting trees
+
+[00:00:00 -829.175292] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00 -519.078739] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078739] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078739] Model parameter optimization (eps = 3.000000)
+[00:00:00 -519.076352] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
+[00:00:00] [worker #1] ML tree search #2, logLikelihood: -519.076351
+[00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
+[00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #1, logLikelihood: -519.076351
+
+[00:00:00 -829.175772] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00 -519.078739] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078739] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078739] Model parameter optimization (eps = 3.000000)
+[00:00:00 -519.076352] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
+[00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
+[00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #3, logLikelihood: -519.076351
+
+[00:00:00 -829.175587] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #4, logLikelihood: -519.076351
+[00:00:00 -519.078739] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078739] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078739] Model parameter optimization (eps = 3.000000)
+[00:00:00 -519.076352] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
+[00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
+[00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #5, logLikelihood: -519.076351
+
+[00:00:00 -829.175772] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00 -519.078738] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078738] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078738] Model parameter optimization (eps = 3.000000)
+[00:00:00] [worker #1] ML tree search #6, logLikelihood: -519.076351
+[00:00:00 -519.076352] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
+[00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
+[00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #7, logLikelihood: -519.076351
+
+[00:00:00 -829.170958] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #8, logLikelihood: -519.076349
+[00:00:00 -519.078738] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078738] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078738] Model parameter optimization (eps = 3.000000)
+[00:00:00 -519.076352] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
+[00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
+[00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #9, logLikelihood: -519.076351
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #10, logLikelihood: -519.076351
+[00:00:00 -519.078739] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078739] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078739] Model parameter optimization (eps = 3.000000)
+[00:00:00 -519.076352] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
+[00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
+[00:00:00] [worker #1] ML tree search #12, logLikelihood: -519.076349
+[00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #11, logLikelihood: -519.076351
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00 -519.078739] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078739] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078739] Model parameter optimization (eps = 3.000000)
+[00:00:00 -519.076352] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
+[00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
+[00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #13, logLikelihood: -519.076351
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00 -519.078739] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078739] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078739] Model parameter optimization (eps = 3.000000)
+[00:00:00] [worker #1] ML tree search #14, logLikelihood: -519.076351
+[00:00:00 -519.076352] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
+[00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
+[00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #15, logLikelihood: -519.076351
+
+[00:00:00 -829.173912] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #16, logLikelihood: -519.076351
+[00:00:00 -519.078738] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078736] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078736] Model parameter optimization (eps = 3.000000)
+[00:00:00 -519.076349] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076349] Model parameter optimization (eps = 1.000000)
+[00:00:00 -519.076349] SLOW spr round 1 (radius: 5)
+[00:00:00 -519.076349] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #17, logLikelihood: -519.076349
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+[00:00:00] [worker #1] ML tree search #18, logLikelihood: -519.076351
+[00:00:00 -519.078739] AUTODETECT spr round 1 (radius: 5)
+[00:00:00 -519.078739] SPR radius for FAST iterations: 5 (autodetect)
+[00:00:00 -519.078739] Model parameter optimization (eps = 3.000000)
+[00:00:00 -519.076352] FAST spr round 1 (radius: 5)
+[00:00:00 -519.076352] Model parameter optimization (eps = 1.000000)
+[00:00:00 -519.076351] SLOW spr round 1 (radius: 5)
+[00:00:00] [worker #1] ML tree search #20, logLikelihood: -519.076349
+[00:00:00 -519.076351] Model parameter optimization (eps = 0.100000)
+
+[00:00:00] [worker #0] ML tree search #19, logLikelihood: -519.076351
+
+
+Optimized model parameters:
+
+   Partition 0: noname
+   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 99.862657 (ML),  weights&rates: (0.250000,0.875823) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897) 
+   Base frequencies (ML): 0.238421 0.269740 0.291564 0.200274 
+   Substitution rates (ML): 0.001000 0.843569 0.001000 0.001000 0.001000 1.000000 
+
+
+Final LogLikelihood: -519.076349
+
+AIC score: 1082.152698 / AICc score: 1085.094559 / BIC score: 1168.070659
+Free parameters (model + branch lengths): 22
+
+WARNING: Best ML tree contains 5 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-1/input-seqs.fa.raxml.bestTreeCollapsed
+Best ML tree saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTree
+All ML trees saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.mlTrees
+Optimized model saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestModel
+
+Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log
+
+Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:54
+
+Elapsed time: 0.164 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-1/input-seqs.fa --msa-format FASTA --ancestral --tree /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/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-1/input-seqs.fa
+[00:00:00] Loaded alignment with 8 taxa and 367 sites
+
+WARNING: Sequences XnaiveX and 13de8675ec are exactly identical!
+WARNING: Sequences XnaiveX and 31e052ee14 are exactly identical!
+WARNING: Sequences XnaiveX and 33aaa62e12 are exactly identical!
+WARNING: Sequences XnaiveX and 4233d708fe are exactly identical!
+WARNING: Sequences XnaiveX and 91796617a0 are exactly identical!
+WARNING: Duplicate sequences found: 5
+
+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-1/input-seqs.fa.raxml.reduced.phy
+
+Alignment comprises 1 partitions and 367 sites
+
+Partition 0: noname
+Model: GTR+FO+G4m
+Alignment sites: 367
+Gaps: 0.00 %
+Invariant sites: 99.46 %
+
+
+NOTE: Binary MSA file already exists: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/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 / 184 / 2944
+[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: -829.175292
+
+[00:00:00 -829.175292] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #1, final logLikelihood: -519.078739
+
+[00:00:00] Tree #2, initial LogLikelihood: -829.173726
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #2, final logLikelihood: -519.078739
+
+[00:00:00] Tree #3, initial LogLikelihood: -829.175772
+
+[00:00:00 -829.175772] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #3, final logLikelihood: -519.078739
+
+[00:00:00] Tree #4, initial LogLikelihood: -829.173726
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #4, final logLikelihood: -519.078738
+
+[00:00:00] Tree #5, initial LogLikelihood: -829.175587
+
+[00:00:00 -829.175587] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #5, final logLikelihood: -519.078739
+
+[00:00:00] Tree #6, initial LogLikelihood: -829.170958
+
+[00:00:00 -829.170958] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #6, final logLikelihood: -519.078737
+
+[00:00:00] Tree #7, initial LogLikelihood: -829.175772
+
+[00:00:00 -829.175772] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #7, final logLikelihood: -519.078738
+
+[00:00:00] Tree #8, initial LogLikelihood: -829.175587
+
+[00:00:00 -829.175587] Initial branch length optimization
+[00:00:00 -524.781299] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #8, final logLikelihood: -519.078736
+
+[00:00:00] Tree #9, initial LogLikelihood: -829.170958
+
+[00:00:00 -829.170958] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #9, final logLikelihood: -519.078738
+
+[00:00:00] Tree #10, initial LogLikelihood: -829.175721
+
+[00:00:00 -829.175721] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #10, final logLikelihood: -519.078738
+
+[00:00:00] Tree #11, initial LogLikelihood: -829.173726
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #11, final logLikelihood: -519.078739
+
+[00:00:00] Tree #12, initial LogLikelihood: -829.176201
+
+[00:00:00 -829.176201] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #12, final logLikelihood: -519.078733
+
+[00:00:00] Tree #13, initial LogLikelihood: -829.173726
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #13, final logLikelihood: -519.078739
+
+[00:00:00] Tree #14, initial LogLikelihood: -829.176201
+
+[00:00:00 -829.176201] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #14, final logLikelihood: -519.078738
+
+[00:00:00] Tree #15, initial LogLikelihood: -829.173726
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #15, final logLikelihood: -519.078739
+
+[00:00:00] Tree #16, initial LogLikelihood: -829.173726
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #16, final logLikelihood: -519.078739
+
+[00:00:00] Tree #17, initial LogLikelihood: -829.173912
+
+[00:00:00 -829.173912] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #17, final logLikelihood: -519.078738
+
+[00:00:00] Tree #18, initial LogLikelihood: -829.176201
+
+[00:00:00 -829.176201] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #18, final logLikelihood: -519.078737
+
+[00:00:00] Tree #19, initial LogLikelihood: -829.173726
+
+[00:00:00 -829.173726] Initial branch length optimization
+[00:00:00 -524.781300] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #19, final logLikelihood: -519.078739
+
+[00:00:00] Tree #20, initial LogLikelihood: -829.176201
+
+[00:00:00 -829.176201] Initial branch length optimization
+[00:00:00 -524.781299] Model parameter optimization (eps = 10.000000)
+
+[00:00:00] Tree #20, final logLikelihood: -519.078735
+
+
+Optimized model parameters:
+
+   Partition 0: noname
+   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 99.862657 (ML),  weights&rates: (0.250000,0.875823) (0.250000,0.964713) (0.250000,1.029567) (0.250000,1.129897) 
+   Base frequencies (ML): 0.238369 0.269737 0.291569 0.200326 
+   Substitution rates (ML): 0.001000 0.929845 0.001000 0.001000 0.001000 1.000000 
+
+Marginal ancestral probabilities saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralProbs
+Reconstructed ancestral sequences saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralStates
+Node-labeled tree saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree
+
+Execution log saved to: /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log
+
+Analysis started: 18-Aug-2025 15:31:54 / finished: 18-Aug-2025 15:31:54
+
+Elapsed time: 0.322 seconds
+

test/ref-results/partition-new-simu/raxml/iclust-1/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-1/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-1/input-seqs.fa --msa-format FASTA --ancestral --tree /home/runner/work/partis/partis/test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree

test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa

@@ -0,0 +1,16 @@
+>XnaiveX
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>162cb1691f
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTAATACGAATACTTCCAGCACTGGGGCCAGGGCATCCTGGTCACCGTCTCCTCAG
+>17f57acf2e
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGATTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>73431a9b10
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGTACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAATTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>73d6c6e558
+CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>948b83fb4d
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGAGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>bf50fa2017
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG
+>c8a90cc3d7
+CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAATCCTTCGGAGAGCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTAGTACAGTGGGAGCACCAACTACAACCCCTCCCTCAATAGTGGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCAGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG