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 01:58:03 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DC2/2_msa/Q68DC2_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DC2/3_mltree/Q68DC2.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DC2/4_raxmlng_ancestral/Q68DC2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674683 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/Q68DC2/2_msa/Q68DC2_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 871 sites WARNING: Sequences tr_A0A1D5PWZ8_A0A1D5PWZ8_CHICK_9031 and tr_G1NCP8_G1NCP8_MELGA_9103 are exactly identical! WARNING: Sequences tr_M3YAX0_M3YAX0_MUSPF_9669 and tr_A0A2Y9IKB6_A0A2Y9IKB6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YD22_M3YD22_MUSPF_9669 and tr_F6XLN1_F6XLN1_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YD22_M3YD22_MUSPF_9669 and tr_A0A2U3XEV4_A0A2U3XEV4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2I3GLQ2_A0A2I3GLQ2_NOMLE_61853 and tr_H2PDK0_H2PDK0_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3GLQ2_A0A2I3GLQ2_NOMLE_61853 and tr_A0A2I3M0R3_A0A2I3M0R3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GLQ2_A0A2I3GLQ2_NOMLE_61853 and tr_A0A2K5LLZ5_A0A2K5LLZ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GLQ2_A0A2I3GLQ2_NOMLE_61853 and tr_A0A2K6BE15_A0A2K6BE15_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GLQ2_A0A2I3GLQ2_NOMLE_61853 and tr_A0A2K5Y1T1_A0A2K5Y1T1_MANLE_9568 are exactly identical! WARNING: Sequences tr_B2W462_B2W462_PYRTR_426418 and tr_A0A317AQL2_A0A317AQL2_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3SG36_G3SG36_GORGO_9595 and sp_Q8IWZ3_ANKH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q1Y0_H2Q1Y0_PANTR_9598 and sp_Q12955_ANK3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QQ51_H2QQ51_PANTR_9598 and sp_Q9ULJ7_ANR50_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QQ51_H2QQ51_PANTR_9598 and tr_A0A2R9CD42_A0A2R9CD42_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7A8P2_K7A8P2_PANTR_9598 and sp_O75179_ANR17_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7A8P2_K7A8P2_PANTR_9598 and tr_A0A2R9BI96_A0A2R9BI96_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6ZXD3_F6ZXD3_HORSE_9796 and tr_H0XRX5_H0XRX5_OTOGA_30611 are exactly identical! WARNING: Sequences tr_A0A158NYD8_A0A158NYD8_ATTCE_12957 and tr_A0A195AYV4_A0A195AYV4_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6ZH85_F6ZH85_MACMU_9544 and tr_A0A2I3N6E9_A0A2I3N6E9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6ZH85_F6ZH85_MACMU_9544 and tr_A0A2K5Y5C2_A0A2K5Y5C2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7EBU2_F7EBU2_MACMU_9544 and tr_A0A2I3NH47_A0A2I3NH47_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H1K0_F7H1K0_MACMU_9544 and tr_G7P687_G7P687_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H1K0_F7H1K0_MACMU_9544 and tr_A0A0D9S0M9_A0A0D9S0M9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7H1K0_F7H1K0_MACMU_9544 and tr_A0A2K5MH73_A0A2K5MH73_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H1K0_F7H1K0_MACMU_9544 and tr_A0A2K6D9V0_A0A2K6D9V0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H1K0_F7H1K0_MACMU_9544 and tr_A0A2K5YBY3_A0A2K5YBY3_MANLE_9568 are exactly identical! WARNING: Sequences tr_D2HEA0_D2HEA0_AILME_9646 and tr_A0A384BYR1_A0A384BYR1_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1LD79_G1LD79_AILME_9646 and tr_A0A384CAR5_A0A384CAR5_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1LX53_G1LX53_AILME_9646 and tr_A0A2U3ZD56_A0A2U3ZD56_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1LX53_G1LX53_AILME_9646 and tr_A0A2U3XJ53_A0A2U3XJ53_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G7PDE9_G7PDE9_MACFA_9541 and tr_A0A2K6CI25_A0A2K6CI25_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PDE9_G7PDE9_MACFA_9541 and tr_A0A2K6ACH1_A0A2K6ACH1_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3XEN9_M3XEN9_FELCA_9685 and tr_A0A2U3WCI4_A0A2U3WCI4_ODORO_9708 are exactly identical! WARNING: Sequences tr_U3K0F9_U3K0F9_FICAL_59894 and tr_A0A091EUN4_A0A091EUN4_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3K0F9_U3K0F9_FICAL_59894 and tr_A0A218UXQ1_A0A218UXQ1_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0Q3PN20_A0A0Q3PN20_AMAAE_12930 and tr_A0A087QKS1_A0A087QKS1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0Q3PN20_A0A0Q3PN20_AMAAE_12930 and tr_A0A093IB22_A0A093IB22_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZH1_A0A2D0SZH1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZW2_A0A2D0SZW2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZW7_A0A2D0SZW7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0T0E7_A0A2D0T0E7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0T0F3_A0A2D0T0F3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4AGJ9_A0A2U4AGJ9_TURTR_9739 and tr_A0A2Y9PPE1_A0A2Y9PPE1_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AGJ9_A0A2U4AGJ9_TURTR_9739 and tr_A0A2Y9SX60_A0A2Y9SX60_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4AGJ9_A0A2U4AGJ9_TURTR_9739 and tr_A0A384B3D1_A0A384B3D1_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4AR74_A0A2U4AR74_TURTR_9739 and tr_A0A383ZBC3_A0A383ZBC3_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3X075_A0A2U3X075_ODORO_9708 and tr_A0A2U3Y629_A0A2U3Y629_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 47 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/Q68DC2/4_raxmlng_ancestral/Q68DC2.raxml.reduced.phy Alignment comprises 1 partitions and 871 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 871 Gaps: 41.55 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DC2/4_raxmlng_ancestral/Q68DC2.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/Q68DC2/3_mltree/Q68DC2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 218 / 17440 [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: -341816.694437 [00:00:00 -341816.694437] Initial branch length optimization [00:00:02 -339119.965089] Model parameter optimization (eps = 0.100000) [00:01:07] Tree #1, final logLikelihood: -337408.305384 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.095280,0.360618) (0.098330,0.356829) (0.364494,0.874524) (0.441896,1.384477) 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/Q68DC2/4_raxmlng_ancestral/Q68DC2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DC2/4_raxmlng_ancestral/Q68DC2.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DC2/4_raxmlng_ancestral/Q68DC2.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DC2/4_raxmlng_ancestral/Q68DC2.raxml.log Analysis started: 03-Jun-2021 01:58:03 / finished: 03-Jun-2021 01:59:19 Elapsed time: 75.797 seconds Consumed energy: 4.493 Wh