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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:38:00 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O14920/2_msa/O14920_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O14920/3_mltree/O14920.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O14920/4_raxmlng_ancestral/O14920 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622648280 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/O14920/2_msa/O14920_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 756 sites WARNING: Sequences tr_M3XPL3_M3XPL3_MUSPF_9669 and tr_F1PD00_F1PD00_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XPL3_M3XPL3_MUSPF_9669 and tr_G1MH77_G1MH77_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XPL3_M3XPL3_MUSPF_9669 and tr_A0A2U3WJZ8_A0A2U3WJZ8_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I2Z3H1_A0A2I2Z3H1_GORGO_9595 and tr_A0A2I3S2D1_A0A2I3S2D1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_H2N9S4_H2N9S4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_H2Q1M3_H2Q1M3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and sp_Q8IU85_KCC1D_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_H9FXH1_H9FXH1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_A0A2K5LSL0_A0A2K5LSL0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_A0A2K6DCE4_A0A2K6DCE4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A088APZ5_A0A088APZ5_APIME_7460 and tr_A0A2A3EIA7_A0A2A3EIA7_APICC_94128 are exactly identical! WARNING: Sequences sp_O14920_IKKB_HUMAN_9606 and tr_A0A2R9B3R9_A0A2R9B3R9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7GKF1_F7GKF1_MACMU_9544 and tr_A0A2I3MXS4_A0A2I3MXS4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GKF1_F7GKF1_MACMU_9544 and tr_A0A2K5XVT4_A0A2K5XVT4_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9EV28_H9EV28_MACMU_9544 and tr_A0A096P352_A0A096P352_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9EV28_H9EV28_MACMU_9544 and tr_A0A0D9R643_A0A0D9R643_CHLSB_60711 are exactly identical! WARNING: Sequences tr_B8AKP1_B8AKP1_ORYSI_39946 and tr_I1P9V3_I1P9V3_ORYGL_4538 are exactly identical! WARNING: Sequences tr_G3SL66_G3SL66_LOXAF_9785 and tr_A0A2Y9DRE8_A0A2Y9DRE8_TRIMA_127582 are exactly identical! WARNING: Sequences tr_F4WEJ1_F4WEJ1_ACREC_103372 and tr_A0A195FL43_A0A195FL43_9HYME_34720 are exactly identical! WARNING: Sequences tr_I3LNH4_I3LNH4_PIG_9823 and tr_A0A2U4B6J6_A0A2U4B6J6_TURTR_9739 are exactly identical! WARNING: Sequences tr_I3LNH4_I3LNH4_PIG_9823 and tr_A0A2Y9T4S3_A0A2Y9T4S3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_I3LNH4_I3LNH4_PIG_9823 and tr_A0A383YXR9_A0A383YXR9_BALAS_310752 are exactly identical! WARNING: Sequences tr_A8WTH2_A8WTH2_CAEBR_6238 and tr_A0A2G5V3L1_A0A2G5V3L1_9PELO_1611254 are exactly identical! WARNING: Sequences tr_G7PDQ9_G7PDQ9_MACFA_9541 and tr_A0A2K6BMV3_A0A2K6BMV3_MACNE_9545 are exactly identical! WARNING: Sequences tr_W2Q687_W2Q687_PHYPN_761204 and tr_W2L624_W2L624_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2R040_W2R040_PHYPN_761204 and tr_W2I5Q7_W2I5Q7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0D3FGP2_A0A0D3FGP2_9ORYZ_65489 and tr_A0A0D9Z561_A0A0D9Z561_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A067HF85_A0A067HF85_CITSI_2711 and tr_V4TC86_V4TC86_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067HF85_A0A067HF85_CITSI_2711 and tr_A0A2H5NY29_A0A2H5NY29_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A096P673_A0A096P673_PAPAN_9555 and tr_A0A2K5NYY3_A0A2K5NYY3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P673_A0A096P673_PAPAN_9555 and tr_A0A2K5Z6K3_A0A2K5Z6K3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9R3M3_A0A0D9R3M3_CHLSB_60711 and tr_A0A2K5NMH2_A0A2K5NMH2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R3M3_A0A0D9R3M3_CHLSB_60711 and tr_A0A2K6DFZ6_A0A2K6DFZ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091V1E2_A0A091V1E2_NIPNI_128390 and tr_A0A087R005_A0A087R005_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A2I0MH53_A0A2I0MH53_COLLI_8932 and tr_A0A1V4K061_A0A1V4K061_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0K0XR56_A0A0K0XR56_TOBAC_4097 and tr_A0A1S4AG40_A0A1S4AG40_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A0K0XR56_A0A0K0XR56_TOBAC_4097 and tr_A0A1U7Y2C5_A0A1U7Y2C5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4B6H6_A0A1S4B6H6_TOBAC_4097 and tr_A0A1U7WUL8_A0A1U7WUL8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1Y1W3J2_A0A1Y1W3J2_9FUNG_1314790 and tr_A0A1Y1YWX3_A0A1Y1YWX3_9FUNG_1314790 are exactly identical! WARNING: Sequences tr_A0A226N9S1_A0A226N9S1_CALSU_9009 and tr_A0A226PZV4_A0A226PZV4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QYM9_A0A2D0QYM9_ICTPU_7998 and tr_A0A2D0R0F0_A0A2D0R0F0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0A7_A0A2D0T0A7_ICTPU_7998 and tr_W5UIG3_W5UIG3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5M0U9_A0A2K5M0U9_CERAT_9531 and tr_A0A2K6DCD6_A0A2K6DCD6_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 43 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/O14920/4_raxmlng_ancestral/O14920.raxml.reduced.phy Alignment comprises 1 partitions and 756 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 756 Gaps: 36.07 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O14920/4_raxmlng_ancestral/O14920.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/O14920/3_mltree/O14920.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 189 / 15120 [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: -295383.725317 [00:00:00 -295383.725317] Initial branch length optimization [00:00:02 -293151.760663] Model parameter optimization (eps = 0.100000) [00:01:07] Tree #1, final logLikelihood: -292121.164078 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.075629,0.275008) (0.107585,0.292686) (0.374425,0.791017) (0.442360,1.472863) 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/O14920/4_raxmlng_ancestral/O14920.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O14920/4_raxmlng_ancestral/O14920.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O14920/4_raxmlng_ancestral/O14920.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O14920/4_raxmlng_ancestral/O14920.raxml.log Analysis started: 02-Jun-2021 18:38:00 / finished: 02-Jun-2021 18:39:14 Elapsed time: 74.671 seconds Consumed energy: 4.477 Wh