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 23-Jun-2021 04:19:51 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q8NFD2/2_msa/Q8NFD2_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q8NFD2/3_mltree/Q8NFD2.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q8NFD2/4_raxmlng_ancestral/Q8NFD2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624411191 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/030621_run/phylogeny-snakemake/results/Q8NFD2/2_msa/Q8NFD2_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 765 sites WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_F7EBU2_F7EBU2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_A0A2I3NH47_A0A2I3NH47_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_G3S4C5_G3S4C5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_H2R3U2_H2R3U2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and sp_Q01484_ANK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_F7H4E0_F7H4E0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_G7P649_G7P649_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A096N0E1_A0A096N0E1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A2K5MCB6_A0A2K5MCB6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A2K5YPQ5_A0A2K5YPQ5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A2R9BUB3_A0A2R9BUB3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A2U3WE70_A0A2U3WE70_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A384BYK5_A0A384BYK5_URSMA_29073 are exactly identical! WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and tr_H2NAT9_H2NAT9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and tr_H2Q1Y0_H2Q1Y0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and sp_Q12955_ANK3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and tr_F7D3K5_F7D3K5_CALJA_9483 are exactly identical! WARNING: Sequences tr_F1PJ98_F1PJ98_CANLF_9615 and tr_G1L9X1_G1L9X1_AILME_9646 are exactly identical! WARNING: Sequences tr_F1PJ98_F1PJ98_CANLF_9615 and tr_A0A2Y9J2Q3_A0A2Y9J2Q3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F1PJ98_F1PJ98_CANLF_9615 and tr_A0A384CIA2_A0A384CIA2_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3RYC1_A0A2I3RYC1_PANTR_9598 and sp_O43353_RIPK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TDL6_A0A2I3TDL6_PANTR_9598 and tr_A0A2R8ZRW6_A0A2R8ZRW6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R3M2_H2R3M2_PANTR_9598 and tr_A0A0D9RRD4_A0A0D9RRD4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2R3M2_H2R3M2_PANTR_9598 and tr_A0A2R9AEU3_A0A2R9AEU3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A087ZZ74_A0A087ZZ74_APIME_7460 and tr_A0A2A3EF29_A0A2A3EF29_APICC_94128 are exactly identical! WARNING: Sequences tr_F6Q6C2_F6Q6C2_MACMU_9544 and tr_A0A2K6DQC0_A0A2K6DQC0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7EV70_F7EV70_MACMU_9544 and tr_A0A2K6B1S8_A0A2K6B1S8_MACNE_9545 are exactly identical! WARNING: Sequences tr_E5S1J1_E5S1J1_TRISP_6334 and tr_A0A0V1D676_A0A0V1D676_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5S1J1_E5S1J1_TRISP_6334 and tr_A0A0V0ZB57_A0A0V0ZB57_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5S1J1_E5S1J1_TRISP_6334 and tr_A0A0V0UDW4_A0A0V0UDW4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A287AUI5_A0A287AUI5_PIG_9823 and tr_A0A337SR04_A0A337SR04_FELCA_9685 are exactly identical! WARNING: Sequences tr_B4MF25_B4MF25_DROVI_7244 and tr_D0Z7C6_D0Z7C6_DROVI_7244 are exactly identical! WARNING: Sequences tr_G7PDE9_G7PDE9_MACFA_9541 and tr_A0A2K5N412_A0A2K5N412_CERAT_9531 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_A0A0V0S5A0_A0A0V0S5A0_9BILA_6336 and tr_A0A0V1P299_A0A0V1P299_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0WNA2_A0A0V0WNA2_9BILA_92179 and tr_A0A0V1LCQ3_A0A0V1LCQ3_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A151J9H4_A0A151J9H4_9HYME_471704 and tr_A0A195F701_A0A195F701_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1D1V615_A0A1D1V615_RAMVA_947166 and tr_A0A1D1VBN2_A0A1D1VBN2_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A1D1V615_A0A1D1V615_RAMVA_947166 and tr_A0A1D1VF84_A0A1D1VF84_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A226NKX9_A0A226NKX9_CALSU_9009 and tr_A0A226PXS3_A0A226PXS3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5NTA2_A0A2K5NTA2_CERAT_9531 and tr_A0A2K5Z8G1_A0A2K5Z8G1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4BEB4_A0A2U4BEB4_TURTR_9739 and tr_A0A2Y9M5I2_A0A2Y9M5I2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BEB4_A0A2U4BEB4_TURTR_9739 and tr_A0A383Z7Q5_A0A383Z7Q5_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 44 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q8NFD2/4_raxmlng_ancestral/Q8NFD2.raxml.reduced.phy Alignment comprises 1 partitions and 765 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 765 Gaps: 29.70 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q8NFD2/4_raxmlng_ancestral/Q8NFD2.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/030621_run/phylogeny-snakemake/results/Q8NFD2/3_mltree/Q8NFD2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 192 / 15360 [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: -341182.562140 [00:00:00 -341182.562140] Initial branch length optimization [00:00:02 -339398.675093] Model parameter optimization (eps = 0.100000) [00:00:52] Tree #1, final logLikelihood: -337449.666679 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.150084,0.623474) (0.082340,0.393471) (0.454307,0.932246) (0.313269,1.438068) 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/030621_run/phylogeny-snakemake/results/Q8NFD2/4_raxmlng_ancestral/Q8NFD2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q8NFD2/4_raxmlng_ancestral/Q8NFD2.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q8NFD2/4_raxmlng_ancestral/Q8NFD2.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q8NFD2/4_raxmlng_ancestral/Q8NFD2.raxml.log Analysis started: 23-Jun-2021 04:19:51 / finished: 23-Jun-2021 04:20:50 Elapsed time: 59.380 seconds Consumed energy: 4.847 Wh