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 12-Jul-2021 17:48:20 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q11203/2_msa/Q11203_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q11203/3_mltree/Q11203.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q11203/4_raxmlng_ancestral/Q11203 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101300 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/300621_run/phylogeny-snakemake/results/Q11203/2_msa/Q11203_nogap_msa.fasta [00:00:00] Loaded alignment with 851 taxa and 375 sites WARNING: Sequences tr_M3YQD8_M3YQD8_MUSPF_9669 and tr_A0A2Y9J1M2_A0A2Y9J1M2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YQD8_M3YQD8_MUSPF_9669 and tr_A0A384CSS7_A0A384CSS7_URSMA_29073 are exactly identical! WARNING: Sequences tr_G3SDW7_G3SDW7_GORGO_9595 and tr_H2Q535_H2Q535_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8R114_A0A2J8R114_PONAB_9601 and sp_Q5RE85_SIA10_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2J8R114_A0A2J8R114_PONAB_9601 and sp_Q9Y274_SIA10_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8R114_A0A2J8R114_PONAB_9601 and tr_G7NZ81_G7NZ81_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2J8WHW4_A0A2J8WHW4_PONAB_9601 and sp_P15907_SIAT1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3S5I3_A0A2I3S5I3_PANTR_9598 and tr_A0A2R9C5E6_A0A2R9C5E6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8LZP5_A0A2J8LZP5_PANTR_9598 and tr_A0A2R9C335_A0A2R9C335_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7B413_K7B413_PANTR_9598 and tr_A0A2R9CAF5_A0A2R9CAF5_PANPA_9597 are exactly identical! WARNING: Sequences sp_P61132_SIAT6_PANTR_9598 and sp_Q11203_SIAT6_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q6KB54_SIA10_PANTR_9598 and tr_A0A2R8Z6P2_A0A2R8Z6P2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5RE99_A0A1D5RE99_MACMU_9544 and tr_G7PD04_G7PD04_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RE99_A0A1D5RE99_MACMU_9544 and tr_A0A2K5L7V5_A0A2K5L7V5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5RE99_A0A1D5RE99_MACMU_9544 and tr_A0A2K6C7V3_A0A2K6C7V3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5RE99_A0A1D5RE99_MACMU_9544 and tr_A0A2K5YXI8_A0A2K5YXI8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6TW24_F6TW24_MACMU_9544 and tr_A0A096N7D3_A0A096N7D3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6TW24_F6TW24_MACMU_9544 and tr_A0A2K5P6T2_A0A2K5P6T2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7A1D7_F7A1D7_MACMU_9544 and tr_G7PMN0_G7PMN0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7A1D7_F7A1D7_MACMU_9544 and tr_A0A2I3N623_A0A2I3N623_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7A1D7_F7A1D7_MACMU_9544 and tr_A0A2K5ZHM5_A0A2K5ZHM5_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9FYK1_H9FYK1_MACMU_9544 and tr_A0A096MNC5_A0A096MNC5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9FYK1_H9FYK1_MACMU_9544 and tr_A0A2K5NIY6_A0A2K5NIY6_CERAT_9531 are exactly identical! WARNING: Sequences tr_H9FYK1_H9FYK1_MACMU_9544 and tr_A0A2K6CLM3_A0A2K6CLM3_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0Z748_H0Z748_TAEGU_59729 and tr_U3JY67_U3JY67_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0Z748_H0Z748_TAEGU_59729 and tr_A0A091FP85_A0A091FP85_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z748_H0Z748_TAEGU_59729 and tr_A0A218V6S9_A0A218V6S9_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZAS5_H0ZAS5_TAEGU_59729 and tr_A0A091J3L2_A0A091J3L2_EGRGA_188379 are exactly identical! WARNING: Sequences tr_K7GPR8_K7GPR8_PIG_9823 and sp_Q02745_SIA4A_PIG_9823 are exactly identical! WARNING: Sequences tr_G7NUX6_G7NUX6_MACFA_9541 and tr_A0A2K5P3Z2_A0A2K5P3Z2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NUX6_G7NUX6_MACFA_9541 and tr_A0A2K6DPH9_A0A2K6DPH9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NUX6_G7NUX6_MACFA_9541 and tr_A0A2K5YDH9_A0A2K5YDH9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7NYN3_G7NYN3_MACFA_9541 and tr_A0A2K6A6C2_A0A2K6A6C2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096N896_A0A096N896_PAPAN_9555 and tr_A0A2K5ZHQ2_A0A2K5ZHQ2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091VD20_A0A091VD20_NIPNI_128390 and tr_A0A087RHI0_A0A087RHI0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A226NLF4_A0A226NLF4_CALSU_9009 and tr_A0A226PJ01_A0A226PJ01_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QNQ7_A0A2D0QNQ7_ICTPU_7998 and tr_A0A2D0QRK9_A0A2D0QRK9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T888_A0A2D0T888_ICTPU_7998 and tr_A0A2D0T8B3_A0A2D0T8B3_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 38 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q11203/4_raxmlng_ancestral/Q11203.raxml.reduced.phy Alignment comprises 1 partitions and 375 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 375 Gaps: 30.38 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q11203/4_raxmlng_ancestral/Q11203.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/300621_run/phylogeny-snakemake/results/Q11203/3_mltree/Q11203.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 94 / 7520 [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: -127352.274818 [00:00:00 -127352.274818] Initial branch length optimization [00:00:00 -126589.409775] Model parameter optimization (eps = 0.100000) [00:00:31] Tree #1, final logLikelihood: -126241.746720 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.103611,0.261204) (0.116250,0.374374) (0.400388,0.821193) (0.379750,1.581617) 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/300621_run/phylogeny-snakemake/results/Q11203/4_raxmlng_ancestral/Q11203.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q11203/4_raxmlng_ancestral/Q11203.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q11203/4_raxmlng_ancestral/Q11203.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q11203/4_raxmlng_ancestral/Q11203.raxml.log Analysis started: 12-Jul-2021 17:48:20 / finished: 12-Jul-2021 17:48:55 Elapsed time: 34.629 seconds Consumed energy: 2.902 Wh