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 12-Jul-2021 17:15:47 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/2_msa/Q96PU5_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/3_mltree/Q96PU5.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/4_raxmlng_ancestral/Q96PU5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099347 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/300621_run/phylogeny-snakemake/results/Q96PU5/2_msa/Q96PU5_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 975 sites WARNING: Sequences tr_E3RQV3_E3RQV3_PYRTT_861557 and tr_B2W179_B2W179_PYRTR_426418 are exactly identical! WARNING: Sequences tr_E3RQV3_E3RQV3_PYRTT_861557 and tr_A0A2W1DRQ7_A0A2W1DRQ7_9PLEO_45151 are exactly identical! WARNING: Sequences tr_J3K9N9_J3K9N9_COCIM_246410 and tr_A0A0J6YB63_A0A0J6YB63_COCIT_404692 are exactly identical! WARNING: Sequences tr_C0NMQ2_C0NMQ2_AJECG_447093 and tr_F0U541_F0U541_AJEC8_544711 are exactly identical! WARNING: Sequences tr_Q7RV01_Q7RV01_NEUCR_367110 and tr_G4UYR6_G4UYR6_NEUT9_510952 are exactly identical! WARNING: Sequences tr_A0A179UHY6_A0A179UHY6_BLAGS_559298 and tr_C5GFJ5_C5GFJ5_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A179UHY6_A0A179UHY6_BLAGS_559298 and tr_A0A1J9PUN1_A0A1J9PUN1_9EURO_1658174 are exactly identical! WARNING: Sequences tr_H2QWD9_H2QWD9_PANTR_9598 and tr_A0A2R9BAH3_A0A2R9BAH3_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BGN1_K7BGN1_PANTR_9598 and sp_Q96J02_ITCH_HUMAN_9606 are exactly identical! WARNING: Sequences tr_E9EJF9_E9EJF9_METRA_655844 and tr_A0A0B4HP08_A0A0B4HP08_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9EJF9_E9EJF9_METRA_655844 and tr_A0A0D9NSU6_A0A0D9NSU6_METAN_1291518 are exactly identical! WARNING: Sequences tr_J4USV8_J4USV8_BEAB2_655819 and tr_A0A2N6P080_A0A2N6P080_BEABA_176275 are exactly identical! WARNING: Sequences sp_A2QQ28_RSP5_ASPNC_425011 and tr_G3YFP8_G3YFP8_ASPNA_380704 are exactly identical! WARNING: Sequences sp_A2QQ28_RSP5_ASPNC_425011 and tr_A0A319A8D3_A0A319A8D3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_G7PGK1_G7PGK1_MACFA_9541 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A096NUS9_A0A096NUS9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A0D9RI42_A0A0D9RI42_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A2K5KTB2_A0A2K5KTB2_CERAT_9531 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A2K6BGS2_A0A2K6BGS2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9ERF6_H9ERF6_MACMU_9544 and tr_A0A2K5Z4A3_A0A2K5Z4A3_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZND1_H0ZND1_TAEGU_59729 and tr_A0A218V5Z2_A0A218V5Z2_9PASE_299123 are exactly identical! WARNING: Sequences tr_F9XPD8_F9XPD8_ZYMTI_336722 and tr_A0A1X7S762_A0A1X7S762_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YHG2_G2YHG2_BOTF4_999810 and tr_M7UZ78_M7UZ78_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_G1LRF3_G1LRF3_AILME_9646 and tr_A0A384CNI5_A0A384CNI5_URSMA_29073 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A0D2XML3_A0A0D2XML3_FUSO4_426428 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_S0E188_S0E188_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_N4U0R5_N4U0R5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_X0C902_X0C902_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A2H3SP11_A0A2H3SP11_FUSOX_5507 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A2H3HCZ8_A0A2H3HCZ8_FUSOX_327505 are exactly identical! WARNING: Sequences tr_W7LYW0_W7LYW0_GIBM7_334819 and tr_A0A2K0WET4_A0A2K0WET4_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A015LXQ7_A0A015LXQ7_9GLOM_1432141 and tr_A0A2I1FVZ7_A0A2I1FVZ7_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A096MQS5_A0A096MQS5_PAPAN_9555 and tr_A0A2K5LPS3_A0A2K5LPS3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A094EJM6_A0A094EJM6_9PEZI_1420912 and tr_A0A1B8GLH3_A0A1B8GLH3_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A087QVU0_A0A087QVU0_APTFO_9233 and tr_A0A0A0AW30_A0A0A0AW30_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0G4P0J5_A0A0G4P0J5_PENCA_1429867 and tr_A0A1V6NEE6_A0A1V6NEE6_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A0L0RZ82_A0A0L0RZ82_ALLMA_578462 and tr_A0A0L0S7E5_A0A0L0S7E5_ALLMA_578462 are exactly identical! WARNING: Sequences tr_A0A1V8SVT2_A0A1V8SVT2_9PEZI_1507870 and tr_A0A1V8T1U8_A0A1V8T1U8_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2K6CED3_A0A2K6CED3_MACNE_9545 and tr_A0A2K6AB02_A0A2K6AB02_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A319CCM8_A0A319CCM8_9EURO_1448315 and tr_A0A2V5IP97_A0A2V5IP97_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A319DWT4_A0A319DWT4_9EURO_1448318 and tr_A0A395GYZ8_A0A395GYZ8_9EURO_1448316 are exactly identical! WARNING: Sequences tr_A0A2Y9T0Z2_A0A2Y9T0Z2_PHYCD_9755 and tr_A0A384B201_A0A384B201_BALAS_310752 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/300621_run/phylogeny-snakemake/results/Q96PU5/4_raxmlng_ancestral/Q96PU5.raxml.reduced.phy Alignment comprises 1 partitions and 975 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 975 Gaps: 27.22 % Invariant sites: 2.26 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/4_raxmlng_ancestral/Q96PU5.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/300621_run/phylogeny-snakemake/results/Q96PU5/3_mltree/Q96PU5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 244 / 19520 [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: -261086.990695 [00:00:00 -261086.990695] Initial branch length optimization [00:00:02 -222802.607393] Model parameter optimization (eps = 0.100000) [00:01:07] Tree #1, final logLikelihood: -222357.861104 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.181366,0.190128) (0.236749,0.316911) (0.277935,0.739801) (0.303950,2.253238) 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/300621_run/phylogeny-snakemake/results/Q96PU5/4_raxmlng_ancestral/Q96PU5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/4_raxmlng_ancestral/Q96PU5.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/4_raxmlng_ancestral/Q96PU5.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96PU5/4_raxmlng_ancestral/Q96PU5.raxml.log Analysis started: 12-Jul-2021 17:15:47 / finished: 12-Jul-2021 17:17:04 Elapsed time: 76.814 seconds Consumed energy: 5.111 Wh