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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 02-Jun-2021 17:53:11 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/2_msa/O95243_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/3_mltree/O95243.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/4_raxmlng_ancestral/O95243 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622645591
  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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/2_msa/O95243_nogap_msa.fasta
[00:00:00] Loaded alignment with 657 taxa and 580 sites

WARNING: Sequences tr_M3YCE2_M3YCE2_MUSPF_9669 and tr_A0A2Y9ILQ5_A0A2Y9ILQ5_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I2ZBB7_A0A2I2ZBB7_GORGO_9595 and tr_K7B3Z3_K7B3Z3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZBB7_A0A2I2ZBB7_GORGO_9595 and sp_P51608_MECP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_B8PP32_B8PP32_POSPM_561896 and tr_A0A1X6N5B3_A0A1X6N5B3_9APHY_670580 are exactly identical!
WARNING: Sequences tr_G1T4T5_G1T4T5_RABIT_9986 and tr_A0A1U7UHV2_A0A1U7UHV2_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_H2R3B9_H2R3B9_PANTR_9598 and sp_O95983_MBD3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R3B9_H2R3B9_PANTR_9598 and tr_A0A0A0MX39_A0A0A0MX39_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2R3B9_H2R3B9_PANTR_9598 and tr_A0A0D9RHS4_A0A0D9RHS4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2R3B9_H2R3B9_PANTR_9598 and tr_A0A2K5P0C0_A0A2K5P0C0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6QCH9_F6QCH9_HORSE_9796 and tr_W5P722_W5P722_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_F6QCH9_F6QCH9_HORSE_9796 and tr_G3N2R6_G3N2R6_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F6QCH9_F6QCH9_HORSE_9796 and tr_A0A337SG34_A0A337SG34_FELCA_9685 are exactly identical!
WARNING: Sequences tr_F6QCH9_F6QCH9_HORSE_9796 and tr_A0A2U3V1S5_A0A2U3V1S5_TURTR_9739 are exactly identical!
WARNING: Sequences tr_F6QCH9_F6QCH9_HORSE_9796 and tr_A0A2U3V234_A0A2U3V234_TURTR_9739 are exactly identical!
WARNING: Sequences tr_F6QCH9_F6QCH9_HORSE_9796 and tr_A0A2U3WK53_A0A2U3WK53_ODORO_9708 are exactly identical!
WARNING: Sequences tr_F6QCH9_F6QCH9_HORSE_9796 and tr_A0A2U3Y6Q6_A0A2U3Y6Q6_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_F6QCH9_F6QCH9_HORSE_9796 and tr_A0A2Y9MKJ4_A0A2Y9MKJ4_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A1D5QTV7_A0A1D5QTV7_MACMU_9544 and tr_G7PWS2_G7PWS2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QTV7_A0A1D5QTV7_MACMU_9544 and tr_A0A2K6D5A2_A0A2K6D5A2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GKH5_F7GKH5_MACMU_9544 and tr_A0A2I3MX28_A0A2I3MX28_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7GKH5_F7GKH5_MACMU_9544 and tr_A0A2K5YNT0_A0A2K5YNT0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_I1QLS5_I1QLS5_ORYGL_4538 and tr_A0A0D3H3E1_A0A0D3H3E1_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_F7HKY5_F7HKY5_CALJA_9483 and tr_G7Q210_G7Q210_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HKY5_F7HKY5_CALJA_9483 and tr_A0A0D9R395_A0A0D9R395_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7HKY5_F7HKY5_CALJA_9483 and tr_A0A2K5KX58_A0A2K5KX58_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HKY5_F7HKY5_CALJA_9483 and tr_A0A2K6AX79_A0A2K6AX79_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F2SVX7_F2SVX7_TRIRC_559305 and tr_A0A178EY97_A0A178EY97_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_A0A1S3X7G8_A0A1S3X7G8_TOBAC_4097 and tr_A0A1U7WGK5_A0A1U7WGK5_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3ZKS4_A0A1S3ZKS4_TOBAC_4097 and tr_A0A1U7XSG5_A0A1U7XSG5_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2D0R0H1_A0A2D0R0H1_ICTPU_7998 and tr_A0A2D0R2M7_A0A2D0R2M7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2Y9M632_A0A2Y9M632_DELLE_9749 and tr_A0A2Y9TJS6_A0A2Y9TJS6_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A383W4M2_A0A383W4M2_TETOB_3088 and tr_A0A383W8M6_A0A383W8M6_TETOB_3088 are exactly identical!
WARNING: Duplicate sequences found: 32

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/4_raxmlng_ancestral/O95243.raxml.reduced.phy

Alignment comprises 1 partitions and 580 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 580
Gaps: 57.56 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/4_raxmlng_ancestral/O95243.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/3_mltree/O95243.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 145 / 11600
[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: -218406.167075

[00:00:00 -218406.167075] Initial branch length optimization
[00:00:02 -182722.415956] Model parameter optimization (eps = 0.100000)

[00:00:59] Tree #1, final logLikelihood: -181882.532136


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.070220,0.346859) (0.055634,0.521138) (0.171946,0.531269) (0.702200,1.218031) 
   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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/4_raxmlng_ancestral/O95243.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/4_raxmlng_ancestral/O95243.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/4_raxmlng_ancestral/O95243.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O95243/4_raxmlng_ancestral/O95243.raxml.log

Analysis started: 02-Jun-2021 17:53:11 / finished: 02-Jun-2021 17:54:14

Elapsed time: 62.838 seconds

Consumed energy: 5.809 Wh