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 13:37:00 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P05089/2_msa/P05089_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P05089/3_mltree/P05089.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P05089/4_raxmlng_ancestral/P05089 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803020 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/P05089/2_msa/P05089_nogap_msa.fasta [00:00:00] Loaded alignment with 926 taxa and 322 sites WARNING: Sequences sp_Q1E180_ARGI_COCIM_246410 and tr_A0A0J7BCU5_A0A0J7BCU5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6Q347_B6Q347_TALMQ_441960 and tr_A0A093XVD8_A0A093XVD8_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WNS5_B2WNS5_PYRTR_426418 and tr_A0A2W1DVD5_A0A2W1DVD5_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3QS73_G3QS73_GORGO_9595 and tr_H2Q8H7_H2Q8H7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QS73_G3QS73_GORGO_9595 and sp_P78540_ARGI2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QS73_G3QS73_GORGO_9595 and tr_A0A2R9CNG5_A0A2R9CNG5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1SG64_G1SG64_RABIT_9986 and sp_Q95KM0_ARGI1_RABIT_9986 are exactly identical! WARNING: Sequences tr_B8N3N6_B8N3N6_ASPFN_332952 and tr_A0A1S9DMF1_A0A1S9DMF1_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UQT0_A0A179UQT0_BLAGS_559298 and tr_C5G7E0_C5G7E0_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QTR0_H2QTR0_PANTR_9598 and tr_A0A2R9AMG0_A0A2R9AMG0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FAK6_F9FAK6_FUSOF_660025 and tr_A0A0D2Y9E5_A0A0D2Y9E5_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FAK6_F9FAK6_FUSOF_660025 and tr_N4UAZ3_N4UAZ3_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FAK6_F9FAK6_FUSOF_660025 and tr_X0CPW1_X0CPW1_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FAK6_F9FAK6_FUSOF_660025 and tr_A0A2H3TV74_A0A2H3TV74_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FAK6_F9FAK6_FUSOF_660025 and tr_A0A2H3H4G3_A0A2H3H4G3_FUSOX_327505 are exactly identical! WARNING: Sequences tr_J5JZ83_J5JZ83_BEAB2_655819 and tr_A0A0A2VQA9_A0A0A2VQA9_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J5JZ83_J5JZ83_BEAB2_655819 and tr_A0A2N6NYB7_A0A2N6NYB7_BEABA_176275 are exactly identical! WARNING: Sequences tr_A2QDI8_A2QDI8_ASPNC_425011 and tr_G3Y3K5_G3Y3K5_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QDI8_A2QDI8_ASPNC_425011 and tr_A0A319BIF7_A0A319BIF7_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F6ULL5_F6ULL5_MACMU_9544 and tr_A0A096P063_A0A096P063_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7C244_F7C244_MACMU_9544 and tr_A0A0D9RLH0_A0A0D9RLH0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7C244_F7C244_MACMU_9544 and tr_A0A2K6BCJ9_A0A2K6BCJ9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7C244_F7C244_MACMU_9544 and tr_A0A2K5YVB6_A0A2K5YVB6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7XPJ9_G7XPJ9_ASPKW_1033177 and tr_A0A117DWG8_A0A117DWG8_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XPJ9_G7XPJ9_ASPKW_1033177 and tr_A0A146FD88_A0A146FD88_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XPJ9_G7XPJ9_ASPKW_1033177 and tr_A0A1L9N7G9_A0A1L9N7G9_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G2XPF0_G2XPF0_BOTF4_999810 and tr_M7UA03_M7UA03_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SVY6_F2SVY6_TRIRC_559305 and tr_A0A178EYW7_A0A178EYW7_TRIRU_5551 are exactly identical! WARNING: Sequences tr_D4B381_D4B381_ARTBC_663331 and tr_A0A059JGB7_A0A059JGB7_9EURO_1215338 are exactly identical! WARNING: Sequences tr_W7N9L8_W7N9L8_GIBM7_334819 and tr_A0A2K0WG47_A0A2K0WG47_GIBNY_42673 are exactly identical! WARNING: Sequences tr_S0EH33_S0EH33_GIBF5_1279085 and tr_A0A365NPY6_A0A365NPY6_GIBIN_948311 are exactly identical! WARNING: Sequences tr_U5HAN8_U5HAN8_USTV1_683840 and tr_A0A2X0PE90_A0A2X0PE90_9BASI_796604 are exactly identical! WARNING: Sequences tr_A0A015IAV1_A0A015IAV1_9GLOM_1432141 and tr_A0A2I1DX26_A0A2I1DX26_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A096NVQ1_A0A096NVQ1_PAPAN_9555 and tr_A0A2K5KS62_A0A2K5KS62_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0F0IGN9_A0A0F0IGN9_ASPPU_1403190 and tr_A0A2G7FJR0_A0A2G7FJR0_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0L0SNH5_A0A0L0SNH5_ALLMA_578462 and tr_A0A0L0SYA8_A0A0L0SYA8_ALLMA_578462 are exactly identical! WARNING: Sequences tr_I1S2H3_I1S2H3_GIBZE_229533 and tr_A0A2T4GYG5_A0A2T4GYG5_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A1L9X9Q0_A0A1L9X9Q0_ASPAC_690307 and tr_A0A319C0J8_A0A319C0J8_9EURO_1448315 are exactly identical! WARNING: Sequences tr_A0A1L9X9Q0_A0A1L9X9Q0_ASPAC_690307 and tr_A0A2V5IFY9_A0A2V5IFY9_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A1L9X9Q0_A0A1L9X9Q0_ASPAC_690307 and tr_A0A2V5H182_A0A2V5H182_9EURO_1450538 are exactly identical! WARNING: Sequences tr_A0A2S7P5I7_A0A2S7P5I7_9HELO_2070414 and tr_A0A2S7QED9_A0A2S7QED9_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2G4SP80_A0A2G4SP80_9FUNG_1340429 and tr_A0A367JVK1_A0A367JVK1_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A2U4A9U1_A0A2U4A9U1_TURTR_9739 and tr_A0A2Y9N3L2_A0A2Y9N3L2_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 43 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/P05089/4_raxmlng_ancestral/P05089.raxml.reduced.phy Alignment comprises 1 partitions and 322 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 322 Gaps: 11.04 % Invariant sites: 0.31 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P05089/4_raxmlng_ancestral/P05089.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/P05089/3_mltree/P05089.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 81 / 6480 [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: -137141.102723 [00:00:00 -137141.102723] Initial branch length optimization [00:00:01 -136971.488982] Model parameter optimization (eps = 0.100000) [00:00:44] Tree #1, final logLikelihood: -136495.820177 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.192892,0.401206) (0.300578,0.479991) (0.297128,0.953331) (0.209403,2.364226) 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/P05089/4_raxmlng_ancestral/P05089.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P05089/4_raxmlng_ancestral/P05089.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P05089/4_raxmlng_ancestral/P05089.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P05089/4_raxmlng_ancestral/P05089.raxml.log Analysis started: 04-Jun-2021 13:37:00 / finished: 04-Jun-2021 13:37:48 Elapsed time: 47.905 seconds