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 01:53:02 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01453/2_msa/Q01453_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01453/3_mltree/Q01453.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01453/4_raxmlng_ancestral/Q01453 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674382 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/Q01453/2_msa/Q01453_nogap_msa.fasta [00:00:00] Loaded alignment with 411 taxa and 160 sites WARNING: Sequences tr_M3XWL4_M3XWL4_MUSPF_9669 and tr_A0A2Y9KZL8_A0A2Y9KZL8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XYI4_M3XYI4_MUSPF_9669 and tr_E2RAX5_E2RAX5_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XYI4_M3XYI4_MUSPF_9669 and tr_A0A2I2V3X9_A0A2I2V3X9_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XYI4_M3XYI4_MUSPF_9669 and tr_A0A2U3WZX9_A0A2U3WZX9_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XYI4_M3XYI4_MUSPF_9669 and tr_A0A2Y9L075_A0A2Y9L075_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1QWG1_G1QWG1_NOMLE_61853 and tr_G3RGJ1_G3RGJ1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QWG1_G1QWG1_NOMLE_61853 and tr_A0A2J8K237_A0A2J8K237_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QWG1_G1QWG1_NOMLE_61853 and tr_F7H5H1_F7H5H1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QWG1_G1QWG1_NOMLE_61853 and tr_A0A0A0MU61_A0A0A0MU61_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QWG1_G1QWG1_NOMLE_61853 and tr_A0A0D9S2S8_A0A0D9S2S8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QWG1_G1QWG1_NOMLE_61853 and tr_A0A2K5MGK8_A0A2K5MGK8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QWG1_G1QWG1_NOMLE_61853 and tr_A0A2R9CBG2_A0A2R9CBG2_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5RAZ3_PMP22_PONAB_9601 and sp_Q01453_PMP22_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5RCY3_EMP1_PONAB_9601 and sp_P54849_EMP1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_A5A6N6_EMP2_PANTR_9598 and tr_A0A2R8ZMQ7_A0A2R8ZMQ7_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6THT0_F6THT0_MACMU_9544 and tr_A0A096NLN2_A0A096NLN2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6THT0_F6THT0_MACMU_9544 and tr_A0A0D9R821_A0A0D9R821_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6THT0_F6THT0_MACMU_9544 and tr_A0A2K6BTM6_A0A2K6BTM6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UPR9_F6UPR9_MACMU_9544 and tr_G7PJX0_G7PJX0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6W2G0_F6W2G0_MACMU_9544 and tr_A0A096P2Z2_A0A096P2Z2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6W2G0_F6W2G0_MACMU_9544 and tr_A0A0D9R9G8_A0A0D9R9G8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6W2G0_F6W2G0_MACMU_9544 and tr_A0A2K6CHU1_A0A2K6CHU1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6W2G0_F6W2G0_MACMU_9544 and tr_A0A2K5Y2M5_A0A2K5Y2M5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5C1H7_G5C1H7_HETGA_10181 and tr_A0A091DYM8_A0A091DYM8_FUKDA_885580 are exactly identical! WARNING: Sequences tr_H0Z2Z6_H0Z2Z6_TAEGU_59729 and tr_A0A218UIN3_A0A218UIN3_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A091VQH8_A0A091VQH8_NIPNI_128390 and tr_A0A0A0A6V0_A0A0A0A6V0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0M726_A0A2I0M726_COLLI_8932 and tr_A0A1V4KWJ1_A0A1V4KWJ1_PATFA_372326 are exactly identical! WARNING: Sequences tr_B5X9J8_B5X9J8_SALSA_8030 and tr_A0A060WNQ5_A0A060WNQ5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A060XZQ3_A0A060XZQ3_ONCMY_8022 and tr_A0A060YCL3_A0A060YCL3_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226NIH2_A0A226NIH2_CALSU_9009 and tr_A0A226PPZ6_A0A226PPZ6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K6B4E5_A0A2K6B4E5_MACNE_9545 and tr_A0A2K6A3H9_A0A2K6A3H9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2Y9F010_A0A2Y9F010_PHYCD_9755 and tr_A0A383YZG4_A0A383YZG4_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 32 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/Q01453/4_raxmlng_ancestral/Q01453.raxml.reduced.phy Alignment comprises 1 partitions and 160 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 160 Gaps: 5.55 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01453/4_raxmlng_ancestral/Q01453.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/Q01453/3_mltree/Q01453.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 40 / 3200 [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: -26973.162201 [00:00:00 -26973.162201] Initial branch length optimization [00:00:00 -26938.944534] Model parameter optimization (eps = 0.100000) [00:00:10] Tree #1, final logLikelihood: -26763.333268 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.271633,0.434899) (0.359568,0.477555) (0.243661,1.217435) (0.125138,3.304441) 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/Q01453/4_raxmlng_ancestral/Q01453.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01453/4_raxmlng_ancestral/Q01453.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01453/4_raxmlng_ancestral/Q01453.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q01453/4_raxmlng_ancestral/Q01453.raxml.log Analysis started: 03-Jun-2021 01:53:02 / finished: 03-Jun-2021 01:53:13 Elapsed time: 11.064 seconds Consumed energy: 0.832 Wh