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 17-Jun-2021 23:59:18 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P55084/2_msa/P55084_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P55084/3_mltree/P55084.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P55084/4_raxmlng_ancestral/P55084 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1623963558 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/P55084/2_msa/P55084_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 474 sites WARNING: Sequences tr_B4QB11_B4QB11_DROSI_7240 and tr_B4I8U9_B4I8U9_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3KKZ5_J3KKZ5_COCIM_246410 and tr_A0A0J6YS57_A0A0J6YS57_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QMG9_B6QMG9_TALMQ_441960 and tr_A0A093UZT2_A0A093UZT2_TALMA_1077442 are exactly identical! WARNING: Sequences tr_Q292R6_Q292R6_DROPS_46245 and tr_B4GCX3_B4GCX3_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NYP6_B8NYP6_ASPFN_332952 and tr_Q2TZ23_Q2TZ23_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NYP6_B8NYP6_ASPFN_332952 and tr_A0A1S9DFU1_A0A1S9DFU1_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UAY1_A0A179UAY1_BLAGS_559298 and tr_C5GIT7_C5GIT7_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2Q4P9_H2Q4P9_PANTR_9598 and sp_P24752_THIL_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q4P9_H2Q4P9_PANTR_9598 and tr_A0A2R9B6L3_A0A2R9B6L3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QMA8_H2QMA8_PANTR_9598 and sp_P09110_THIK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_A0A0D2XPN3_A0A0D2XPN3_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_N4U1B1_N4U1B1_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_X0C154_X0C154_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_A0A2H3TLS2_A0A2H3TLS2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_A0A2H3HKY2_A0A2H3HKY2_FUSOX_327505 are exactly identical! WARNING: Sequences tr_E9F9M7_E9F9M7_METRA_655844 and tr_A0A0D9NVY0_A0A0D9NVY0_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6HG02_C6HG02_AJECH_544712 and tr_F0UMQ8_F0UMQ8_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A2R924_A2R924_ASPNC_425011 and tr_G3Y6Z5_G3Y6Z5_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R924_A2R924_ASPNC_425011 and tr_A0A318ZTL9_A0A318ZTL9_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F6VM61_F6VM61_MACMU_9544 and tr_A0A2K6CYM6_A0A2K6CYM6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XC62_F6XC62_MACMU_9544 and tr_G7PNQ8_G7PNQ8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XC62_F6XC62_MACMU_9544 and tr_A0A2K6CWR8_A0A2K6CWR8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XQX4_G7XQX4_ASPKW_1033177 and tr_A0A100ILS4_A0A100ILS4_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XQX4_G7XQX4_ASPKW_1033177 and tr_A0A146FTY3_A0A146FTY3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XQX4_G7XQX4_ASPKW_1033177 and tr_A0A1L9N574_A0A1L9N574_ASPTU_767770 are exactly identical! WARNING: Sequences tr_F4NXY0_F4NXY0_BATDJ_684364 and tr_A0A177WMG2_A0A177WMG2_BATDE_403673 are exactly identical! WARNING: Sequences tr_F4P8H3_F4P8H3_BATDJ_684364 and tr_A0A177WTF7_A0A177WTF7_BATDE_403673 are exactly identical! WARNING: Sequences tr_E3N068_E3N068_CAERE_31234 and tr_A0A260ZVE4_A0A260ZVE4_9PELO_1503980 are exactly identical! WARNING: Sequences tr_F2SIK2_F2SIK2_TRIRC_559305 and tr_A0A178F307_A0A178F307_TRIRU_5551 are exactly identical! WARNING: Sequences tr_S0DW03_S0DW03_GIBF5_1279085 and tr_A0A365NEH3_A0A365NEH3_GIBIN_948311 are exactly identical! WARNING: Sequences tr_U5HHC8_U5HHC8_USTV1_683840 and tr_A0A2X0NE55_A0A2X0NE55_9BASI_796604 are exactly identical! WARNING: Sequences tr_W2R7C5_W2R7C5_PHYPN_761204 and tr_A0A0W8D613_A0A0W8D613_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R7C5_W2R7C5_PHYPN_761204 and tr_W2L5E2_W2L5E2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A096NFA1_A0A096NFA1_PAPAN_9555 and tr_A0A0D9RPI0_A0A0D9RPI0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NFA1_A0A096NFA1_PAPAN_9555 and tr_A0A2K6B4M4_A0A2K6B4M4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NW84_A0A096NW84_PAPAN_9555 and tr_A0A0D9R8S0_A0A0D9R8S0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NW84_A0A096NW84_PAPAN_9555 and tr_A0A2K5XCJ8_A0A2K5XCJ8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A094DUZ4_A0A094DUZ4_9PEZI_1420912 and tr_A0A1B8GAD1_A0A1B8GAD1_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F8W419_A0A0F8W419_9EURO_308745 and tr_A0A2T5M5H1_A0A2T5M5H1_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0A1N7C7_A0A0A1N7C7_9FUNG_58291 and tr_A0A367JLP4_A0A367JLP4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0V0WG79_A0A0V0WG79_9BILA_92179 and tr_A0A0V1LA86_A0A0V1LA86_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WG79_A0A0V0WG79_9BILA_92179 and tr_A0A0V1NW77_A0A0V1NW77_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0WG79_A0A0V0WG79_9BILA_92179 and tr_A0A0V0U5Z7_A0A0V0U5Z7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S4CHI1_A0A1S4CHI1_TOBAC_4097 and tr_A0A1U7UU15_A0A1U7UU15_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2V5HMP9_A0A2V5HMP9_9EURO_1450541 and tr_A0A2V5H2A4_A0A2V5H2A4_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 45 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/P55084/4_raxmlng_ancestral/P55084.raxml.reduced.phy Alignment comprises 1 partitions and 474 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 474 Gaps: 17.14 % Invariant sites: 0.21 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P55084/4_raxmlng_ancestral/P55084.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/P55084/3_mltree/P55084.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 119 / 9520 [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: -177608.335914 [00:00:00 -177608.335914] Initial branch length optimization [00:00:01 -177086.143079] Model parameter optimization (eps = 0.100000) [00:00:28] Tree #1, final logLikelihood: -176435.756169 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.199665,0.355277) (0.273790,0.457255) (0.263073,1.027987) (0.263472,2.024641) 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/P55084/4_raxmlng_ancestral/P55084.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P55084/4_raxmlng_ancestral/P55084.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P55084/4_raxmlng_ancestral/P55084.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P55084/4_raxmlng_ancestral/P55084.raxml.log Analysis started: 17-Jun-2021 23:59:18 / finished: 17-Jun-2021 23:59:51 Elapsed time: 32.472 seconds Consumed energy: 2.204 Wh