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 03-Jun-2021 01:40:11 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35557/2_msa/P35557_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35557/3_mltree/P35557.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35557/4_raxmlng_ancestral/P35557 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622673611 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/P35557/2_msa/P35557_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 465 sites WARNING: Sequences tr_M3XZC2_M3XZC2_MUSPF_9669 and tr_A0A2Y9J5I8_A0A2Y9J5I8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YAC2_M3YAC2_MUSPF_9669 and tr_A0A2Y9JGA5_A0A2Y9JGA5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_B2WN00_B2WN00_PYRTR_426418 and tr_A0A2W1FSB2_A0A2W1FSB2_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3R9K6_G3R9K6_GORGO_9595 and sp_Q2TB90_HKDC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R9K6_G3R9K6_GORGO_9595 and tr_A0A2R9B419_A0A2R9B419_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RIM9_G3RIM9_GORGO_9595 and tr_H2Q206_H2Q206_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RIM9_G3RIM9_GORGO_9595 and tr_A0A2R9C115_A0A2R9C115_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q293D3_Q293D3_DROPS_46245 and tr_B4GBV6_B4GBV6_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NPD5_B8NPD5_ASPFN_332952 and tr_Q2UML5_Q2UML5_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NPD5_B8NPD5_ASPFN_332952 and tr_Q9HGZ3_Q9HGZ3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_F9FR13_F9FR13_FUSOF_660025 and tr_N4TWT4_N4TWT4_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A158NYM9_A0A158NYM9_ATTCE_12957 and tr_A0A195B1Y3_A0A195B1Y3_9HYME_520822 are exactly identical! WARNING: Sequences sp_P52789_HXK2_HUMAN_9606 and tr_A0A2R9BNP9_A0A2R9BNP9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0I9NBR7_A0A0I9NBR7_BRUMA_6279 and tr_A0A0N4T1V7_A0A0N4T1V7_BRUPA_6280 are exactly identical! WARNING: Sequences tr_F6PLG6_F6PLG6_MACMU_9544 and tr_A0A2K5ZSK3_A0A2K5ZSK3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6Q724_F6Q724_MACMU_9544 and tr_A0A2I3M1B3_A0A2I3M1B3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Q724_F6Q724_MACMU_9544 and tr_A0A2K5P7M9_A0A2K5P7M9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Q724_F6Q724_MACMU_9544 and tr_A0A2K6B881_A0A2K6B881_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6Q724_F6Q724_MACMU_9544 and tr_A0A2K5Y9G8_A0A2K5Y9G8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6Y855_F6Y855_MACMU_9544 and tr_G8F2Q5_G8F2Q5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6Y855_F6Y855_MACMU_9544 and tr_A0A2K6CP15_A0A2K6CP15_MACNE_9545 are exactly identical! WARNING: Sequences tr_F4NVW6_F4NVW6_BATDJ_684364 and tr_A0A177WJ30_A0A177WJ30_BATDE_403673 are exactly identical! WARNING: Sequences tr_F9XDZ5_F9XDZ5_ZYMTI_336722 and tr_A0A1X7RX07_A0A1X7RX07_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F1SNW8_F1SNW8_PIG_9823 and sp_Q1W674_HXK2_PIG_9823 are exactly identical! WARNING: Sequences tr_E3LN77_E3LN77_CAERE_31234 and tr_A0A261BME4_A0A261BME4_9PELO_1503980 are exactly identical! WARNING: Sequences tr_S0DPE1_S0DPE1_GIBF5_1279085 and tr_A0A365N6G6_A0A365N6G6_GIBIN_948311 are exactly identical! WARNING: Sequences tr_A0A096MS63_A0A096MS63_PAPAN_9555 and tr_A0A0D9RTE8_A0A0D9RTE8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MS63_A0A096MS63_PAPAN_9555 and tr_A0A2K5M6A2_A0A2K5M6A2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P4Z5_A0A096P4Z5_PAPAN_9555 and tr_A0A0D9R642_A0A0D9R642_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A0F0I6Y0_A0A0F0I6Y0_ASPPU_1403190 and tr_A0A2G7FX47_A0A2G7FX47_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A2I0MFB9_A0A2I0MFB9_COLLI_8932 and tr_A0A1V4KJY4_A0A1V4KJY4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1V8UN50_A0A1V8UN50_9PEZI_1974281 and tr_A0A1V8SS12_A0A1V8SS12_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A226N8F0_A0A226N8F0_CALSU_9009 and tr_A0A226P4F6_A0A226P4F6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3ST42_A0A2H3ST42_FUSOX_5507 and tr_A0A2H3HV68_A0A2H3HV68_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A2H3ST42_A0A2H3ST42_FUSOX_5507 and tr_A0A2K0W502_A0A2K0W502_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A2K5P4J6_A0A2K5P4J6_CERAT_9531 and tr_A0A2K5XNY8_A0A2K5XNY8_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 36 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/P35557/4_raxmlng_ancestral/P35557.raxml.reduced.phy Alignment comprises 1 partitions and 465 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 465 Gaps: 9.71 % Invariant sites: 0.22 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35557/4_raxmlng_ancestral/P35557.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/P35557/3_mltree/P35557.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 117 / 9360 [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: -190117.687635 [00:00:00 -190117.687635] Initial branch length optimization [00:00:01 -188207.146503] Model parameter optimization (eps = 0.100000) [00:00:26] Tree #1, final logLikelihood: -187443.228396 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.195552,0.333160) (0.274782,0.378956) (0.238418,0.995451) (0.291249,2.037389) 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/P35557/4_raxmlng_ancestral/P35557.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35557/4_raxmlng_ancestral/P35557.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35557/4_raxmlng_ancestral/P35557.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35557/4_raxmlng_ancestral/P35557.raxml.log Analysis started: 03-Jun-2021 01:40:11 / finished: 03-Jun-2021 01:40:43 Elapsed time: 31.420 seconds Consumed energy: 2.405 Wh