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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:55:43 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/2_msa/Q8TDZ2_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/3_mltree/Q8TDZ2.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/4_raxmlng_ancestral/Q8TDZ2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804143 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/2_msa/Q8TDZ2_nogap_msa.fasta [00:00:00] Loaded alignment with 986 taxa and 1067 sites WARNING: Sequences sp_Q9JI91_ACTN2_MOUSE_10090 and tr_D3ZCV0_D3ZCV0_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YMU0_M3YMU0_MUSPF_9669 and tr_E2QUQ0_E2QUQ0_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A179U8Q2_A0A179U8Q2_BLAGS_559298 and tr_C5GIP3_C5GIP3_AJEDR_559297 are exactly identical! WARNING: Sequences tr_K7CTI8_K7CTI8_PANTR_9598 and tr_A0A2R8ZU41_A0A2R8ZU41_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NGS2_A0A158NGS2_ATTCE_12957 and tr_A0A195BVX4_A0A195BVX4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NGS2_A0A158NGS2_ATTCE_12957 and tr_A0A195EU35_A0A195EU35_9HYME_34720 are exactly identical! WARNING: Sequences sp_O94851_MICA2_HUMAN_9606 and tr_A0A2R9BD02_A0A2R9BD02_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_G7PQP9_G7PQP9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_A0A2I3MTK1_A0A2I3MTK1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_A0A2K5P755_A0A2K5P755_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_A0A2K6CGD9_A0A2K6CGD9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_A0A2K6AI94_A0A2K6AI94_MANLE_9568 are exactly identical! WARNING: Sequences tr_E3LNI9_E3LNI9_CAERE_31234 and tr_A0A261AGW2_A0A261AGW2_9PELO_1503980 are exactly identical! WARNING: Sequences tr_B3S0V2_B3S0V2_TRIAD_10228 and tr_A0A369SBW8_A0A369SBW8_9METZ_287889 are exactly identical! WARNING: Sequences sp_F1MF74_MICA2_BOVIN_9913 and tr_H9GW33_H9GW33_BOVIN_9913 are exactly identical! WARNING: Sequences tr_L0P961_L0P961_PNEJ8_1209962 and tr_A0A0W4ZTP2_A0A0W4ZTP2_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_W2QC39_W2QC39_PHYPN_761204 and tr_W2LBL6_W2LBL6_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QIL9_W2QIL9_PHYPN_761204 and tr_A0A0W8DJ24_A0A0W8DJ24_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A059IXW0_A0A059IXW0_9EURO_1215338 and tr_A0A178F4W9_A0A178F4W9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A096NVY8_A0A096NVY8_PAPAN_9555 and tr_A0A2K5LG92_A0A2K5LG92_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0V1D9G3_A0A0V1D9G3_TRIBR_45882 and tr_A0A0V1L6U6_A0A0V1L6U6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D9G3_A0A0V1D9G3_TRIBR_45882 and tr_A0A0V1A0K1_A0A0V1A0K1_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1MMA7_A0A0V1MMA7_9BILA_268474 and tr_A0A0V1HR16_A0A0V1HR16_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V1P1R2_A0A0V1P1R2_9BILA_92180 and tr_A0A0V0U8Q0_A0A0V0U8Q0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1I7T9I0_A0A1I7T9I0_9PELO_1561998 and tr_A0A1I7T9I1_A0A1I7T9I1_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2D0RIC0_A0A2D0RIC0_ICTPU_7998 and tr_A0A2D0RIC2_A0A2D0RIC2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RIC0_A0A2D0RIC0_ICTPU_7998 and tr_A0A2D0RJF1_A0A2D0RJF1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RIC0_A0A2D0RIC0_ICTPU_7998 and tr_A0A2D0RK17_A0A2D0RK17_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RJF6_A0A2D0RJF6_ICTPU_7998 and tr_A0A2D0RK22_A0A2D0RK22_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RQD2_A0A2D0RQD2_ICTPU_7998 and tr_A0A2D0RR08_A0A2D0RR08_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RTA7_A0A2D0RTA7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RTB4_A0A2D0RTB4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RTB9_A0A2D0RTB9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RU88_A0A2D0RU88_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RU96_A0A2D0RU96_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RUU7_A0A2D0RUU7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RUV1_A0A2D0RUV1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RUV6_A0A2D0RUV6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3WWF0_A0A2U3WWF0_ODORO_9708 and tr_A0A2U3Y3N1_A0A2U3Y3N1_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 39 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/4_raxmlng_ancestral/Q8TDZ2.raxml.reduced.phy Alignment comprises 1 partitions and 1067 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1067 Gaps: 42.96 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/4_raxmlng_ancestral/Q8TDZ2.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/3_mltree/Q8TDZ2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 267 / 21360 [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: -353369.510583 [00:00:00 -353369.510583] Initial branch length optimization [00:00:02 -331682.923963] Model parameter optimization (eps = 0.100000) [00:01:15] Tree #1, final logLikelihood: -329825.831061 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.186772,0.546467) (0.092266,0.632761) (0.318254,0.699100) (0.402708,1.532279) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/4_raxmlng_ancestral/Q8TDZ2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/4_raxmlng_ancestral/Q8TDZ2.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/4_raxmlng_ancestral/Q8TDZ2.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8TDZ2/4_raxmlng_ancestral/Q8TDZ2.raxml.log Analysis started: 04-Jun-2021 13:55:43 / finished: 04-Jun-2021 13:57:07 Elapsed time: 84.277 seconds