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 02-Jun-2021 18:27:33 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IZJ4/2_msa/Q8IZJ4_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IZJ4/3_mltree/Q8IZJ4.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IZJ4/4_raxmlng_ancestral/Q8IZJ4 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647653 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/Q8IZJ4/2_msa/Q8IZJ4_nogap_msa.fasta [00:00:00] Loaded alignment with 851 taxa and 473 sites WARNING: Sequences tr_E3RSC8_E3RSC8_PYRTT_861557 and tr_A0A2W1D4W2_A0A2W1D4W2_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3QLM7_G3QLM7_GORGO_9595 and sp_Q12967_GNDS_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SBI2_G3SBI2_GORGO_9595 and tr_H2PL57_H2PL57_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SBI2_G3SBI2_GORGO_9595 and sp_O15211_RGL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q7RYH5_Q7RYH5_NEUCR_367110 and tr_G4UN20_G4UN20_NEUT9_510952 are exactly identical! WARNING: Sequences tr_H2QST2_H2QST2_PANTR_9598 and tr_A0A2R9AD27_A0A2R9AD27_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7B6P4_K7B6P4_PANTR_9598 and tr_A0A2R9B0Q8_A0A2R9B0Q8_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_W7MGS0_W7MGS0_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_A0A0D2XZS4_A0A0D2XZS4_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_S0E933_S0E933_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_N4UP53_N4UP53_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_X0CVA0_X0CVA0_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_A0A2H3TI72_A0A2H3TI72_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_A0A2K0WIC3_A0A2K0WIC3_GIBNY_42673 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_A0A365MX41_A0A365MX41_GIBIN_948311 are exactly identical! WARNING: Sequences tr_A0A158NLU0_A0A158NLU0_ATTCE_12957 and tr_A0A151HZC5_A0A151HZC5_9HYME_520822 are exactly identical! WARNING: Sequences tr_F7FZA2_F7FZA2_MACMU_9544 and tr_G8F2X7_G8F2X7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FZA2_F7FZA2_MACMU_9544 and tr_A0A0D9RJS7_A0A0D9RJS7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7FZA2_F7FZA2_MACMU_9544 and tr_A0A2K5NVK2_A0A2K5NVK2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FZA2_F7FZA2_MACMU_9544 and tr_A0A2K6ALS1_A0A2K6ALS1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FZA2_F7FZA2_MACMU_9544 and tr_A0A2K6A6I7_A0A2K6A6I7_MANLE_9568 are exactly identical! WARNING: Sequences tr_D4B420_D4B420_ARTBC_663331 and tr_F2PQN2_F2PQN2_TRIEC_559882 are exactly identical! WARNING: Sequences tr_D4B420_D4B420_ARTBC_663331 and tr_A0A059JCD6_A0A059JCD6_9EURO_1215338 are exactly identical! WARNING: Sequences tr_D4B420_D4B420_ARTBC_663331 and tr_A0A178EXK8_A0A178EXK8_TRIRU_5551 are exactly identical! WARNING: Sequences tr_L2FLU1_L2FLU1_COLFN_1213859 and tr_T0LVA2_T0LVA2_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M2SS38_M2SS38_COCSN_665912 and tr_M2SRF6_M2SRF6_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2SS38_M2SS38_COCSN_665912 and tr_W6YIL7_W6YIL7_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2SS38_M2SS38_COCSN_665912 and tr_W6ZIU5_W6ZIU5_COCMI_930090 are exactly identical! WARNING: Sequences tr_U5H6T6_U5H6T6_USTV1_683840 and tr_A0A2X0NUI3_A0A2X0NUI3_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2X632_V2X632_MONRO_1381753 and tr_A0A0W0F3E3_A0A0W0F3E3_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A010S691_A0A010S691_9PEZI_1445577 and tr_A0A135SR12_A0A135SR12_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_A0A010S691_A0A010S691_9PEZI_1445577 and tr_A0A1G4BGV9_A0A1G4BGV9_9PEZI_1209926 are exactly identical! WARNING: Sequences tr_A0A096NHH4_A0A096NHH4_PAPAN_9555 and tr_A0A0D9RB31_A0A0D9RB31_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NHH4_A0A096NHH4_PAPAN_9555 and tr_A0A2K5LMY4_A0A2K5LMY4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NHH4_A0A096NHH4_PAPAN_9555 and tr_A0A2K6D5T7_A0A2K6D5T7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0V1CAU9_A0A0V1CAU9_TRIBR_45882 and tr_A0A0V0UPU6_A0A0V0UPU6_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CAU9_A0A0V1CAU9_TRIBR_45882 and tr_A0A0V1KVJ4_A0A0V1KVJ4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CAU9_A0A0V1CAU9_TRIBR_45882 and tr_A0A0V1NHF7_A0A0V1NHF7_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CAU9_A0A0V1CAU9_TRIBR_45882 and tr_A0A0V0TRM1_A0A0V0TRM1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1I7TD96_A0A1I7TD96_9PELO_1561998 and tr_A0A1I7TD97_A0A1I7TD97_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2D0SYU2_A0A2D0SYU2_ICTPU_7998 and tr_A0A2D0SZ95_A0A2D0SZ95_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3VP87_A0A2U3VP87_ODORO_9708 and tr_A0A384CXC7_A0A384CXC7_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 42 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/Q8IZJ4/4_raxmlng_ancestral/Q8IZJ4.raxml.reduced.phy Alignment comprises 1 partitions and 473 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 473 Gaps: 29.45 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IZJ4/4_raxmlng_ancestral/Q8IZJ4.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/Q8IZJ4/3_mltree/Q8IZJ4.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: -174443.548123 [00:00:00 -174443.548123] Initial branch length optimization [00:00:01 -172238.534061] Model parameter optimization (eps = 0.100000) [00:00:45] Tree #1, final logLikelihood: -171593.765805 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.159351,0.503362) (0.070911,0.615416) (0.295341,0.702444) (0.474397,1.409555) 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/Q8IZJ4/4_raxmlng_ancestral/Q8IZJ4.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IZJ4/4_raxmlng_ancestral/Q8IZJ4.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IZJ4/4_raxmlng_ancestral/Q8IZJ4.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IZJ4/4_raxmlng_ancestral/Q8IZJ4.raxml.log Analysis started: 02-Jun-2021 18:27:33 / finished: 02-Jun-2021 18:28:22 Elapsed time: 49.264 seconds Consumed energy: 2.651 Wh