RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 19-Jul-2021 13:21:04 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/2_msa/P81274_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/3_mltree/P81274.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/4_raxmlng_ancestral/P81274 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626690064
  tip-inner: ON
  pattern compression: OFF
  per-rate scalers: OFF
  site repeats: OFF
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/2_msa/P81274_nogap_msa.fasta
[00:00:00] Loaded alignment with 798 taxa and 684 sites

WARNING: Sequences tr_B4QXH8_B4QXH8_DROSI_7240 and tr_B4IGT6_B4IGT6_DROSE_7238 are exactly identical!
WARNING: Sequences tr_M3YA20_M3YA20_MUSPF_9669 and tr_A0A2Y9L8G8_A0A2Y9L8G8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I2Z2Z3_A0A2I2Z2Z3_GORGO_9595 and tr_H2QF67_H2QF67_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Z2Z3_A0A2I2Z2Z3_GORGO_9595 and sp_Q8IVA1_PCP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Z2Z3_A0A2I2Z2Z3_GORGO_9595 and tr_A0A0D9R7L3_A0A0D9R7L3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2P3X5_H2P3X5_PONAB_9601 and sp_Q96AY4_TTC28_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q29BH6_Q29BH6_DROPS_46245 and tr_B4GNY6_B4GNY6_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2R056_H2R056_PANTR_9598 and tr_A0A2R9CCI0_A0A2R9CCI0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3ZI88_M3ZI88_XIPMA_8083 and tr_A0A087Y6S1_A0A087Y6S1_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A088AH84_A0A088AH84_APIME_7460 and tr_A0A2A3ESD1_A0A2A3ESD1_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_G7PQ94_G7PQ94_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A096N391_A0A096N391_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A0D9R0F1_A0A0D9R0F1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A2K5NVN1_A0A2K5NVN1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A2K6BER0_A0A2K6BER0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QXF2_A0A1D5QXF2_MACMU_9544 and tr_A0A2K5ZHM1_A0A2K5ZHM1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6QN66_F6QN66_MACMU_9544 and tr_A0A096NRH6_A0A096NRH6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6QN66_F6QN66_MACMU_9544 and tr_A0A0D9RC91_A0A0D9RC91_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6QN66_F6QN66_MACMU_9544 and tr_A0A2K5LRW8_A0A2K5LRW8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7NN97_G7NN97_MACMU_9544 and tr_A0A2K6CZ80_A0A2K6CZ80_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A087R8S7_A0A087R8S7_APTFO_9233 and tr_A0A0A0ANF2_A0A0A0ANF2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V0X029_A0A0V0X029_9BILA_92179 and tr_A0A0V1L6Y6_A0A0V1L6Y6_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A151J940_A0A151J940_9HYME_471704 and tr_A0A195BF00_A0A195BF00_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A151J940_A0A151J940_9HYME_471704 and tr_A0A195FEE0_A0A195FEE0_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A226MUX3_A0A226MUX3_CALSU_9009 and tr_A0A226PZV8_A0A226PZV8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0SR43_A0A2D0SR43_ICTPU_7998 and tr_A0A2D0SR57_A0A2D0SR57_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SR43_A0A2D0SR43_ICTPU_7998 and tr_A0A2D0SR60_A0A2D0SR60_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 27

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/4_raxmlng_ancestral/P81274.raxml.reduced.phy

Alignment comprises 1 partitions and 684 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 684
Gaps: 32.36 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/4_raxmlng_ancestral/P81274.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/3_mltree/P81274.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 171 / 13680
[00:00:00] Data distribution: max. searches per worker: 1

Starting ML tree search with 1 distinct starting trees

[00:00:00] Tree #1, initial LogLikelihood: -225332.890390

[00:00:00 -225332.890390] Initial branch length optimization
[00:00:01 -220962.403398] Model parameter optimization (eps = 0.100000)

[00:00:45] Tree #1, final logLikelihood: -220002.279161


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.106243,0.586253) (0.027046,0.542547) (0.461149,0.689800) (0.405562,1.491609) 
   Base frequencies (model): 
M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 
M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 
M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 
M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 
   Substitution rates (model): 
M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 
M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 
M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 
M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 

Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/4_raxmlng_ancestral/P81274.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/4_raxmlng_ancestral/P81274.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/4_raxmlng_ancestral/P81274.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P81274/4_raxmlng_ancestral/P81274.raxml.log

Analysis started: 19-Jul-2021 13:21:04 / finished: 19-Jul-2021 13:21:54

Elapsed time: 50.393 seconds