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 03-Jun-2021 02:18:03 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P02730/2_msa/P02730_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P02730/3_mltree/P02730.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P02730/4_raxmlng_ancestral/P02730 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675883 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/P02730/2_msa/P02730_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 911 sites WARNING: Sequences tr_M3YD88_M3YD88_MUSPF_9669 and tr_A0A2Y9JK10_A0A2Y9JK10_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1S7T8_G1S7T8_NOMLE_61853 and tr_G3R9D5_G3R9D5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S7T8_G1S7T8_NOMLE_61853 and tr_H2NHB6_H2NHB6_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S7T8_G1S7T8_NOMLE_61853 and tr_H2Q5Y3_H2Q5Y3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S7T8_G1S7T8_NOMLE_61853 and tr_F7HME6_F7HME6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S7T8_G1S7T8_NOMLE_61853 and tr_A0A0D9R0P3_A0A0D9R0P3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S7T8_G1S7T8_NOMLE_61853 and tr_A0A2K5M6F7_A0A2K5M6F7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S7T8_G1S7T8_NOMLE_61853 and tr_A0A2R9AN33_A0A2R9AN33_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YW19_A0A2I2YW19_GORGO_9595 and tr_A0A2I3SID8_A0A2I3SID8_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YW19_A0A2I2YW19_GORGO_9595 and tr_A0A2K5LSQ2_A0A2K5LSQ2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RYI6_G3RYI6_GORGO_9595 and tr_A0A2I3RHF2_A0A2I3RHF2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RYI6_G3RYI6_GORGO_9595 and tr_A0A096MUV2_A0A096MUV2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RYI6_G3RYI6_GORGO_9595 and tr_A0A2K5KJF4_A0A2K5KJF4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RYI6_G3RYI6_GORGO_9595 and tr_A0A2K6AHU5_A0A2K6AHU5_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2PBB0_H2PBB0_PONAB_9601 and sp_Q9Y6M7_S4A7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1SR51_G1SR51_RABIT_9986 and sp_Q9XSZ4_S4A4_RABIT_9986 are exactly identical! WARNING: Sequences tr_H2QVM4_H2QVM4_PANTR_9598 and sp_P04920_B3A2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P48751_B3A3_HUMAN_9606 and tr_A0A0D9R699_A0A0D9R699_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q6U841_S4A10_HUMAN_9606 and tr_A0A0D9RSZ5_A0A0D9RSZ5_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q6U841_S4A10_HUMAN_9606 and tr_A0A2K6CC84_A0A2K6CC84_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QDA6_A0A1D5QDA6_MACMU_9544 and tr_A0A2I3MYK2_A0A2I3MYK2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QDA6_A0A1D5QDA6_MACMU_9544 and tr_A0A2K5NZ98_A0A2K5NZ98_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QDA6_A0A1D5QDA6_MACMU_9544 and tr_A0A2K6CXN5_A0A2K6CXN5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FRN6_F7FRN6_MACMU_9544 and tr_G7P5M4_G7P5M4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MNG7_G7MNG7_MACMU_9544 and tr_A0A2I3M8T7_A0A2I3M8T7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MNG7_G7MNG7_MACMU_9544 and tr_A0A0D9R2Z3_A0A0D9R2Z3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7MNG7_G7MNG7_MACMU_9544 and tr_A0A2K5NQ15_A0A2K5NQ15_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MNG7_G7MNG7_MACMU_9544 and tr_A0A2K5YK84_A0A2K5YK84_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1LHJ5_G1LHJ5_AILME_9646 and tr_A0A384CAD4_A0A384CAD4_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A091J967_A0A091J967_EGRGA_188379 and tr_A0A091UUE6_A0A091UUE6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A2I0MJ05_A0A2I0MJ05_COLLI_8932 and tr_A0A1V4K7T0_A0A1V4K7T0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1D5J8_A0A0V1D5J8_TRIBR_45882 and tr_A0A0V0WRF1_A0A0V0WRF1_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1D5J8_A0A0V1D5J8_TRIBR_45882 and tr_A0A0V0VSU7_A0A0V0VSU7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D5J8_A0A0V1D5J8_TRIBR_45882 and tr_A0A0V0UGT8_A0A0V0UGT8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1L882_A0A0V1L882_9BILA_6335 and tr_A0A0V1A4R3_A0A0V1A4R3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A226MW33_A0A226MW33_CALSU_9009 and tr_A0A226NYL8_A0A226NYL8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RA90_A0A2D0RA90_ICTPU_7998 and tr_A0A2D0RA94_A0A2D0RA94_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SF59_A0A2D0SF59_ICTPU_7998 and tr_A0A2D0SFV8_A0A2D0SFV8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SF59_A0A2D0SF59_ICTPU_7998 and tr_A0A2D0SGH0_A0A2D0SGH0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K6CDN0_A0A2K6CDN0_MACNE_9545 and tr_A0A2K5XCX4_A0A2K5XCX4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3ZQJ2_A0A2U3ZQJ2_ODORO_9708 and tr_A0A2Y9JGG0_A0A2Y9JGG0_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 41 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/P02730/4_raxmlng_ancestral/P02730.raxml.reduced.phy Alignment comprises 1 partitions and 911 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 911 Gaps: 12.49 % Invariant sites: 0.11 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P02730/4_raxmlng_ancestral/P02730.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/P02730/3_mltree/P02730.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 228 / 18240 [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: -254689.215750 [00:00:00 -254689.215750] Initial branch length optimization [00:00:02 -253879.284395] Model parameter optimization (eps = 0.100000) [00:00:59] Tree #1, final logLikelihood: -252712.509816 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.273836,0.393771) (0.268763,0.559783) (0.280095,1.166270) (0.177307,2.340894) 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/P02730/4_raxmlng_ancestral/P02730.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P02730/4_raxmlng_ancestral/P02730.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P02730/4_raxmlng_ancestral/P02730.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P02730/4_raxmlng_ancestral/P02730.raxml.log Analysis started: 03-Jun-2021 02:18:03 / finished: 03-Jun-2021 02:19:12 Elapsed time: 68.775 seconds Consumed energy: 4.704 Wh