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 18:30:28 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25067/2_msa/P25067_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25067/3_mltree/P25067.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25067/4_raxmlng_ancestral/P25067 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647828 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/P25067/2_msa/P25067_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 703 sites WARNING: Sequences tr_E1C353_E1C353_CHICK_9031 and tr_A0A226MP62_A0A226MP62_CALSU_9009 are exactly identical! WARNING: Sequences tr_M3YIR4_M3YIR4_MUSPF_9669 and tr_A0A2Y9JJZ8_A0A2Y9JJZ8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3H3E1_A0A2I3H3E1_NOMLE_61853 and tr_G3RE09_G3RE09_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3H3E1_A0A2I3H3E1_NOMLE_61853 and tr_A0A2J8T8T5_A0A2J8T8T5_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3H3E1_A0A2I3H3E1_NOMLE_61853 and sp_P27658_CO8A1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3H3E1_A0A2I3H3E1_NOMLE_61853 and tr_A0A2R9C581_A0A2R9C581_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3HMN0_G3HMN0_CRIGR_10029 and tr_A0A1U7QM18_A0A1U7QM18_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QMG5_G3QMG5_GORGO_9595 and tr_H2N802_H2N802_PONAB_9601 are exactly identical! WARNING: Sequences tr_K7C8P4_K7C8P4_PANTR_9598 and tr_A0A2R8ZQ62_A0A2R8ZQ62_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7C8W0_K7C8W0_PANTR_9598 and tr_A0A2R9AHH5_A0A2R9AHH5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7EQ13_F7EQ13_MACMU_9544 and tr_A0A2K5N4L3_A0A2K5N4L3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_G7NZH7_G7NZH7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_A0A2K5MIM6_A0A2K5MIM6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_A0A2K6B809_A0A2K6B809_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_A0A2K5YA30_A0A2K5YA30_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7H1M7_F7H1M7_MACMU_9544 and tr_G7NZ83_G7NZ83_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H1M7_F7H1M7_MACMU_9544 and tr_A0A096NCC1_A0A096NCC1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H1M7_F7H1M7_MACMU_9544 and tr_A0A0D9R128_A0A0D9R128_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7H1M7_F7H1M7_MACMU_9544 and tr_A0A2K5NJX4_A0A2K5NJX4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H1M7_F7H1M7_MACMU_9544 and tr_A0A2K6BGQ3_A0A2K6BGQ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H1M7_F7H1M7_MACMU_9544 and tr_A0A2K5ZG48_A0A2K5ZG48_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1LBQ9_G1LBQ9_AILME_9646 and tr_A0A384CZG4_A0A384CZG4_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7NTL3_G7NTL3_MACFA_9541 and tr_A0A2K6D175_A0A2K6D175_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MYV1_A0A096MYV1_PAPAN_9555 and tr_A0A2K5LV71_A0A2K5LV71_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MYV1_A0A096MYV1_PAPAN_9555 and tr_A0A2K6DXS5_A0A2K6DXS5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MYV1_A0A096MYV1_PAPAN_9555 and tr_A0A2K6AK27_A0A2K6AK27_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3N198_A0A2I3N198_PAPAN_9555 and tr_A0A0D9RZL4_A0A0D9RZL4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3N198_A0A2I3N198_PAPAN_9555 and tr_A0A2K5M607_A0A2K5M607_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151MD73_A0A151MD73_ALLMI_8496 and tr_A0A1U7S1E2_A0A1U7S1E2_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0V1CJB6_A0A0V1CJB6_TRIBR_45882 and tr_A0A0V0UNG2_A0A0V0UNG2_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CJV7_A0A0V1CJV7_TRIBR_45882 and tr_A0A0V1LSG4_A0A0V1LSG4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CJV7_A0A0V1CJV7_TRIBR_45882 and tr_A0A0V0U3N2_A0A0V0U3N2_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1I7TZH0_A0A1I7TZH0_9PELO_1561998 and tr_A0A1I7TZH2_A0A1I7TZH2_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A226MTY1_A0A226MTY1_CALSU_9009 and tr_A0A226PPF8_A0A226PPF8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0STI6_A0A2D0STI6_ICTPU_7998 and tr_A0A2D0SU10_A0A2D0SU10_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0STI6_A0A2D0STI6_ICTPU_7998 and tr_A0A2D0SUL4_A0A2D0SUL4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LN90_A0A2K5LN90_CERAT_9531 and tr_A0A2K5ZTB1_A0A2K5ZTB1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3V601_A0A2U3V601_TURTR_9739 and tr_A0A2Y9NFH1_A0A2Y9NFH1_DELLE_9749 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/020621_run/phylogeny-snakemake/results/P25067/4_raxmlng_ancestral/P25067.raxml.reduced.phy Alignment comprises 1 partitions and 703 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 703 Gaps: 35.62 % Invariant sites: 1.14 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25067/4_raxmlng_ancestral/P25067.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/P25067/3_mltree/P25067.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 176 / 14080 [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: -351064.718993 [00:00:00 -351064.718993] Initial branch length optimization [00:00:04 -318146.036898] Model parameter optimization (eps = 0.100000) [00:01:41] Tree #1, final logLikelihood: -317391.100830 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.053574,0.320818) (0.297522,0.377528) (0.113163,0.468881) (0.535741,1.525793) 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/P25067/4_raxmlng_ancestral/P25067.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25067/4_raxmlng_ancestral/P25067.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25067/4_raxmlng_ancestral/P25067.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25067/4_raxmlng_ancestral/P25067.raxml.log Analysis started: 02-Jun-2021 18:30:28 / finished: 02-Jun-2021 18:32:16 Elapsed time: 108.558 seconds Consumed energy: 6.821 Wh