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 04-Jun-2021 14:22:31 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEP3/2_msa/Q8NEP3_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEP3/3_mltree/Q8NEP3.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEP3/4_raxmlng_ancestral/Q8NEP3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805751 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_020621/phylogeny-snakemake/results/Q8NEP3/2_msa/Q8NEP3_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 725 sites WARNING: Sequences tr_J3KEH5_J3KEH5_COCIM_246410 and tr_A0A0J7B5D0_A0A0J7B5D0_COCIT_404692 are exactly identical! WARNING: Sequences tr_A0A2I2Z2R3_A0A2I2Z2R3_GORGO_9595 and tr_A0A2I3SG93_A0A2I3SG93_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z2R3_A0A2I2Z2R3_GORGO_9595 and sp_Q15435_PP1R7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Z2R3_A0A2I2Z2R3_GORGO_9595 and tr_A0A096ND99_A0A096ND99_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2Z2R3_A0A2I2Z2R3_GORGO_9595 and tr_A0A2K5KVN4_A0A2K5KVN4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2Z2R3_A0A2I2Z2R3_GORGO_9595 and tr_A0A2K6AQ95_A0A2K6AQ95_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2Z2R3_A0A2I2Z2R3_GORGO_9595 and tr_A0A2R9BXW6_A0A2R9BXW6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2HES2_G2HES2_PANTR_9598 and tr_A0A2R9BRX6_A0A2R9BRX6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2H2IHI9_A0A2H2IHI9_CAEJA_281687 and tr_A0A2H2JMP1_A0A2H2JMP1_CAEJA_281687 are exactly identical! WARNING: Sequences sp_Q8IUZ0_LRC49_HUMAN_9606 and tr_A0A2R9CFT5_A0A2R9CFT5_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q2UKC9_Q2UKC9_ASPOR_510516 and tr_A0A0F0IEL2_A0A0F0IEL2_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_Q2UKC9_Q2UKC9_ASPOR_510516 and tr_A0A1S9DMH3_A0A1S9DMH3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_Q2UKC9_Q2UKC9_ASPOR_510516 and tr_A0A2G7G2X5_A0A2G7G2X5_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0E0G283_A0A0E0G283_ORYNI_4536 and tr_A0A0D9Z390_A0A0D9Z390_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F7E701_F7E701_MACMU_9544 and tr_G7PRJ2_G7PRJ2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GPY4_F7GPY4_MACMU_9544 and tr_G7P908_G7P908_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GPY4_F7GPY4_MACMU_9544 and tr_A0A2I3NEC3_A0A2I3NEC3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GPY4_F7GPY4_MACMU_9544 and tr_A0A0D9RMK3_A0A0D9RMK3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GPY4_F7GPY4_MACMU_9544 and tr_A0A2K6DR73_A0A2K6DR73_MACNE_9545 are exactly identical! WARNING: Sequences tr_A2XDE5_A2XDE5_ORYSI_39946 and tr_A0A0E0NQU1_A0A0E0NQU1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_F4PEN2_F4PEN2_BATDJ_684364 and tr_A0A177WSB1_A0A177WSB1_BATDE_403673 are exactly identical! WARNING: Sequences tr_B3RSJ4_B3RSJ4_TRIAD_10228 and tr_A0A369SHJ4_A0A369SHJ4_9METZ_287889 are exactly identical! WARNING: Sequences tr_W2QY44_W2QY44_PHYPN_761204 and tr_W2K8R8_W2K8R8_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QZU2_W2QZU2_PHYPN_761204 and tr_A0A0W8DYA4_A0A0W8DYA4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QZU2_W2QZU2_PHYPN_761204 and tr_W2K6Q2_W2K6Q2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0G4PLE8_A0A0G4PLE8_PENCA_1429867 and tr_A0A1V6NJP6_A0A1V6NJP6_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A2I0LMG7_A0A2I0LMG7_COLLI_8932 and tr_A0A1V4J4V9_A0A1V4J4V9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0VHV5_A0A0V0VHV5_9BILA_181606 and tr_A0A0V1P5I0_A0A0V1P5I0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0VHV5_A0A0V0VHV5_9BILA_181606 and tr_A0A0V0UFK9_A0A0V0UFK9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A226MTQ6_A0A226MTQ6_CALSU_9009 and tr_A0A226PV10_A0A226PV10_COLVI_9014 are exactly identical! WARNING: Duplicate sequences found: 30 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEP3/4_raxmlng_ancestral/Q8NEP3.raxml.reduced.phy Alignment comprises 1 partitions and 725 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 725 Gaps: 51.12 % Invariant sites: 0.69 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEP3/4_raxmlng_ancestral/Q8NEP3.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_020621/phylogeny-snakemake/results/Q8NEP3/3_mltree/Q8NEP3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 182 / 14560 [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: -358434.762610 [00:00:00 -358434.762610] Initial branch length optimization [00:00:02 -335433.931948] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -334449.413179 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.066984,0.306907) (0.038545,0.238061) (0.224630,0.583059) (0.669841,1.252974) 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_020621/phylogeny-snakemake/results/Q8NEP3/4_raxmlng_ancestral/Q8NEP3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEP3/4_raxmlng_ancestral/Q8NEP3.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEP3/4_raxmlng_ancestral/Q8NEP3.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEP3/4_raxmlng_ancestral/Q8NEP3.raxml.log Analysis started: 04-Jun-2021 14:22:31 / finished: 04-Jun-2021 14:23:19 Elapsed time: 47.507 seconds