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 01:22:24 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O76090/2_msa/O76090_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O76090/3_mltree/O76090.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O76090/4_raxmlng_ancestral/O76090 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622672544 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/O76090/2_msa/O76090_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 585 sites WARNING: Sequences tr_B4QKM0_B4QKM0_DROSI_7240 and tr_B4HI69_B4HI69_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3QS90_G3QS90_GORGO_9595 and tr_H2PYW4_H2PYW4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QS90_G3QS90_GORGO_9595 and sp_Q8NFU0_BEST4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8LVA4_A0A2J8LVA4_PANTR_9598 and sp_Q8NFU1_BEST2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8LVA4_A0A2J8LVA4_PANTR_9598 and tr_A0A2R9BDZ5_A0A2R9BDZ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158P011_A0A158P011_ATTCE_12957 and tr_A0A151I5J9_A0A151I5J9_9HYME_520822 are exactly identical! WARNING: Sequences tr_E5S8M3_E5S8M3_TRISP_6334 and tr_A0A0V0SCI7_A0A0V0SCI7_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5S8M3_E5S8M3_TRISP_6334 and tr_A0A0V1DCJ3_A0A0V1DCJ3_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5S8M3_E5S8M3_TRISP_6334 and tr_A0A0V0VWM8_A0A0V0VWM8_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5S8M3_E5S8M3_TRISP_6334 and tr_A0A0V1LKD5_A0A0V1LKD5_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5S8M3_E5S8M3_TRISP_6334 and tr_A0A0V1A866_A0A0V1A866_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5S8M3_E5S8M3_TRISP_6334 and tr_A0A0V1PF77_A0A0V1PF77_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5S8M3_E5S8M3_TRISP_6334 and tr_A0A0V0UIZ8_A0A0V0UIZ8_9BILA_144512 are exactly identical! WARNING: Sequences tr_E3LG85_E3LG85_CAERE_31234 and tr_A0A261AAC0_A0A261AAC0_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3M7S2_E3M7S2_CAERE_31234 and tr_E3NPZ2_E3NPZ2_CAERE_31234 are exactly identical! WARNING: Sequences tr_E3MT18_E3MT18_CAERE_31234 and tr_A0A261CFT9_A0A261CFT9_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3NLW3_E3NLW3_CAERE_31234 and tr_A0A261C7N1_A0A261C7N1_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A0A0D9R2N2_A0A0D9R2N2_CHLSB_60711 and tr_A0A2K5Z9I0_A0A2K5Z9I0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9S7H1_A0A0D9S7H1_CHLSB_60711 and tr_A0A2K5NRF7_A0A2K5NRF7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9S7H1_A0A0D9S7H1_CHLSB_60711 and tr_A0A2K5YK94_A0A2K5YK94_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0V1DIP9_A0A0V1DIP9_TRIBR_45882 and tr_A0A0V0X5R6_A0A0V0X5R6_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DIP9_A0A0V1DIP9_TRIBR_45882 and tr_A0A0V1LVD8_A0A0V1LVD8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DIP9_A0A0V1DIP9_TRIBR_45882 and tr_A0A0V1PP85_A0A0V1PP85_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DIP9_A0A0V1DIP9_TRIBR_45882 and tr_A0A0V0UDD9_A0A0V0UDD9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0W7D3_A0A0V0W7D3_9BILA_92179 and tr_A0A0V1LG20_A0A0V1LG20_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0W7D3_A0A0V0W7D3_9BILA_92179 and tr_A0A0V1NJ89_A0A0V1NJ89_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0X6B5_A0A0V0X6B5_9BILA_92179 and tr_A0A0V1LUP2_A0A0V1LUP2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0UR64_A0A0V0UR64_9BILA_181606 and tr_A0A0V1AGG2_A0A0V1AGG2_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0UR64_A0A0V0UR64_9BILA_181606 and tr_A0A0V1NV86_A0A0V1NV86_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0UR64_A0A0V0UR64_9BILA_181606 and tr_A0A0V0TKN4_A0A0V0TKN4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0VV04_A0A0V0VV04_9BILA_181606 and tr_A0A0V0TG34_A0A0V0TG34_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1N836_A0A0V1N836_9BILA_268474 and tr_A0A0V1HKH5_A0A0V1HKH5_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0M3QWT7_A0A0M3QWT7_DROBS_30019 and tr_A0A0M4F0J8_A0A0M4F0J8_DROBS_30019 are exactly identical! WARNING: Sequences tr_A0A1I7TX86_A0A1I7TX86_9PELO_1561998 and tr_A0A1I7TX87_A0A1I7TX87_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2K6AZS5_A0A2K6AZS5_MACNE_9545 and tr_A0A2K6AC77_A0A2K6AC77_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 35 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/O76090/4_raxmlng_ancestral/O76090.raxml.reduced.phy Alignment comprises 1 partitions and 585 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 585 Gaps: 30.23 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O76090/4_raxmlng_ancestral/O76090.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/O76090/3_mltree/O76090.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 147 / 11760 [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: -238359.698646 [00:00:00 -238359.698646] Initial branch length optimization [00:00:01 -233691.357530] Model parameter optimization (eps = 0.100000) [00:00:43] Tree #1, final logLikelihood: -233182.533452 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.119584,0.281162) (0.176359,0.357416) (0.294039,0.665895) (0.410018,1.725644) 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/O76090/4_raxmlng_ancestral/O76090.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O76090/4_raxmlng_ancestral/O76090.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O76090/4_raxmlng_ancestral/O76090.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O76090/4_raxmlng_ancestral/O76090.raxml.log Analysis started: 03-Jun-2021 01:22:24 / finished: 03-Jun-2021 01:23:13 Elapsed time: 48.916 seconds Consumed energy: 3.393 Wh