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 12-Jul-2021 17:14:32 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC78/2_msa/Q9HC78_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC78/3_mltree/Q9HC78.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC78/4_raxmlng_ancestral/Q9HC78 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099272 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/Q9HC78/2_msa/Q9HC78_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 741 sites WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_J9NZD8_J9NZD8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_F6UAE9_F6UAE9_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_W5PCH7_W5PCH7_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_G1LSL0_G1LSL0_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_E1BMZ4_E1BMZ4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_A0A2K5YGK7_A0A2K5YGK7_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_A0A2U3Y1N2_A0A2U3Y1N2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_A0A2Y9KFZ4_A0A2Y9KFZ4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_A0A384CDE3_A0A384CDE3_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_A0A2J8SJ28_A0A2J8SJ28_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_H2R0W5_H2R0W5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_I3LY64_I3LY64_ICTTR_43179 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_F7GDG2_F7GDG2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_A0A2I2UHS2_A0A2I2UHS2_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_A0A096MVU8_A0A096MVU8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_A0A0D9S896_A0A0D9S896_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_A0A1U7U3Z7_A0A1U7U3Z7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_A0A2K5LPR7_A0A2K5LPR7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_A0A2K6BKJ1_A0A2K6BKJ1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_A0A2R9BGK0_A0A2R9BGK0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3REJ6_G3REJ6_GORGO_9595 and tr_H2RBQ5_H2RBQ5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3REJ6_G3REJ6_GORGO_9595 and tr_A0A2R9B4T7_A0A2R9B4T7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T5G3_A0A2I3T5G3_PANTR_9598 and sp_Q6P2D0_ZFP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8JLK3_A0A2J8JLK3_PANTR_9598 and sp_Q96NG8_ZN582_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8JLK3_A0A2J8JLK3_PANTR_9598 and tr_A0A2R9A954_A0A2R9A954_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PYV9_H2PYV9_PANTR_9598 and sp_P17025_ZN182_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q9HC78_ZBT20_HUMAN_9606 and tr_A0A2R9B2C7_A0A2R9B2C7_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6WPL2_F6WPL2_MACMU_9544 and tr_A0A2K6DSI0_A0A2K6DSI0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6YLL1_F6YLL1_MACMU_9544 and tr_G7PZ18_G7PZ18_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7D328_F7D328_MACMU_9544 and tr_G7Q2M0_G7Q2M0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7D328_F7D328_MACMU_9544 and tr_A0A2I3N8I2_A0A2I3N8I2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7D328_F7D328_MACMU_9544 and tr_A0A2K6E2S4_A0A2K6E2S4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7D328_F7D328_MACMU_9544 and tr_A0A2K5XRB6_A0A2K5XRB6_MANLE_9568 are exactly identical! WARNING: Sequences tr_Q29RN3_Q29RN3_BOVIN_9913 and tr_A0A2U4C0M9_A0A2U4C0M9_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A096NS05_A0A096NS05_PAPAN_9555 and tr_A0A0D9QUP7_A0A0D9QUP7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P1R1_A0A096P1R1_PAPAN_9555 and tr_A0A2K6AK49_A0A2K6AK49_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MU74_A0A0A0MU74_PAPAN_9555 and tr_A0A2K6DGH3_A0A2K6DGH3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0A0MW60_A0A0A0MW60_PAPAN_9555 and tr_A0A2K5YBB4_A0A2K5YBB4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9S667_A0A0D9S667_CHLSB_60711 and tr_A0A2K5MPF9_A0A2K5MPF9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091JF88_A0A091JF88_EGRGA_188379 and tr_A0A091X0D5_A0A091X0D5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JF88_A0A091JF88_EGRGA_188379 and tr_A0A087RJE9_A0A087RJE9_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JF88_A0A091JF88_EGRGA_188379 and tr_A0A093HWH9_A0A093HWH9_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JF88_A0A091JF88_EGRGA_188379 and tr_A0A0A0ADZ7_A0A0A0ADZ7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2K5N5Y3_A0A2K5N5Y3_CERAT_9531 and tr_A0A2K5XNG6_A0A2K5XNG6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5NUP6_A0A2K5NUP6_CERAT_9531 and tr_A0A2K6D1B4_A0A2K6D1B4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2Y9LKY1_A0A2Y9LKY1_DELLE_9749 and tr_A0A383ZJ36_A0A383ZJ36_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 46 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/Q9HC78/4_raxmlng_ancestral/Q9HC78.raxml.reduced.phy Alignment comprises 1 partitions and 741 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 741 Gaps: 58.29 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC78/4_raxmlng_ancestral/Q9HC78.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/Q9HC78/3_mltree/Q9HC78.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 186 / 14880 [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: -233713.600518 [00:00:00 -233713.600518] Initial branch length optimization [00:00:02 -228666.206295] Model parameter optimization (eps = 0.100000) [00:01:09] Tree #1, final logLikelihood: -227805.310086 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.104555,0.212451) (0.056403,0.417818) (0.285656,0.666005) (0.553386,1.380542) 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/Q9HC78/4_raxmlng_ancestral/Q9HC78.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC78/4_raxmlng_ancestral/Q9HC78.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC78/4_raxmlng_ancestral/Q9HC78.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC78/4_raxmlng_ancestral/Q9HC78.raxml.log Analysis started: 12-Jul-2021 17:14:32 / finished: 12-Jul-2021 17:15:48 Elapsed time: 76.223 seconds Consumed energy: 4.774 Wh