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 02:46:29 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54868/2_msa/P54868_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54868/3_mltree/P54868.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54868/4_raxmlng_ancestral/P54868 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677589 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/P54868/2_msa/P54868_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 508 sites WARNING: Sequences tr_A0A2I3GM62_A0A2I3GM62_NOMLE_61853 and tr_F7HQ90_F7HQ90_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GM62_A0A2I3GM62_NOMLE_61853 and tr_G7P7G3_G7P7G3_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3GM62_A0A2I3GM62_NOMLE_61853 and tr_A0A096NFC3_A0A096NFC3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GM62_A0A2I3GM62_NOMLE_61853 and tr_A0A0D9RW39_A0A0D9RW39_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GM62_A0A2I3GM62_NOMLE_61853 and tr_A0A2K5N2F1_A0A2K5N2F1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GM62_A0A2I3GM62_NOMLE_61853 and tr_A0A2K6BGN5_A0A2K6BGN5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GM62_A0A2I3GM62_NOMLE_61853 and tr_A0A2K6AG93_A0A2K6AG93_MANLE_9568 are exactly identical! WARNING: Sequences tr_B6Q1E0_B6Q1E0_TALMQ_441960 and tr_A0A093V9X5_A0A093V9X5_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WF02_B2WF02_PYRTR_426418 and tr_A0A2W1I1S1_A0A2W1I1S1_9PLEO_45151 are exactly identical! WARNING: Sequences tr_Q1K5Z3_Q1K5Z3_NEUCR_367110 and tr_G4UYP5_G4UYP5_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q291S8_Q291S8_DROPS_46245 and tr_B4GAB9_B4GAB9_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NWD4_B8NWD4_ASPFN_332952 and tr_A0A1S9DEY7_A0A1S9DEY7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UVH8_A0A179UVH8_BLAGS_559298 and tr_C5G9X5_C5G9X5_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A2J8JUL8_A0A2J8JUL8_PANTR_9598 and tr_A0A2R9ASK2_A0A2R9ASK2_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FNY8_F9FNY8_FUSOF_660025 and tr_A0A0D2XPT8_A0A0D2XPT8_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FNY8_F9FNY8_FUSOF_660025 and tr_N4UHZ7_N4UHZ7_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FNY8_F9FNY8_FUSOF_660025 and tr_X0CZB4_X0CZB4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FNY8_F9FNY8_FUSOF_660025 and tr_A0A2H3TAA5_A0A2H3TAA5_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FNY8_F9FNY8_FUSOF_660025 and tr_A0A2H3HLD3_A0A2H3HLD3_FUSOX_327505 are exactly identical! WARNING: Sequences tr_Q2UKZ2_Q2UKZ2_ASPOR_510516 and tr_A0A1S9DN44_A0A1S9DN44_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0IK50_A0A0E0IK50_ORYNI_4536 and tr_B8ALW2_B8ALW2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IK50_A0A0E0IK50_ORYNI_4536 and tr_I1P6X9_I1P6X9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0IK50_A0A0E0IK50_ORYNI_4536 and tr_A0A0D3FD24_A0A0D3FD24_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0IK50_A0A0E0IK50_ORYNI_4536 and tr_A3ADI5_A3ADI5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QD99_A2QD99_ASPNC_425011 and tr_G3Y3D2_G3Y3D2_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QD99_A2QD99_ASPNC_425011 and tr_A0A319AUK4_A0A319AUK4_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A2QN35_A2QN35_ASPNC_425011 and tr_G3XYK8_G3XYK8_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QN35_A2QN35_ASPNC_425011 and tr_A0A319BHB5_A0A319BHB5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X4V5_G7X4V5_ASPKW_1033177 and tr_A0A146FNT6_A0A146FNT6_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7X4V5_G7X4V5_ASPKW_1033177 and tr_A0A317VUS6_A0A317VUS6_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A2Z381_A2Z381_ORYSI_39946 and tr_A0A0E0B5G6_A0A0E0B5G6_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1QQJ7_I1QQJ7_ORYGL_4538 and tr_A0A0D3H915_A0A0D3H915_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_F9X3D9_F9X3D9_ZYMTI_336722 and tr_A0A1X7RIG5_A0A1X7RIG5_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F2SF72_F2SF72_TRIRC_559305 and tr_A0A178ETZ1_A0A178ETZ1_TRIRU_5551 are exactly identical! WARNING: Sequences tr_W7M2P1_W7M2P1_GIBM7_334819 and tr_A0A2K0WU58_A0A2K0WU58_GIBNY_42673 are exactly identical! WARNING: Sequences tr_L0PC82_L0PC82_PNEJ8_1209962 and tr_A0A0W4ZL95_A0A0W4ZL95_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_L2G780_L2G780_COLFN_1213859 and tr_T0KP02_T0KP02_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M7ZBG0_M7ZBG0_TRIUA_4572 and tr_A0A3B6KRF3_A0A3B6KRF3_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067EYG9_A0A067EYG9_CITSI_2711 and tr_V4RLH6_V4RLH6_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067EYG9_A0A067EYG9_CITSI_2711 and tr_A0A2H5NM75_A0A2H5NM75_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A078FJU0_A0A078FJU0_BRANA_3708 and tr_A0A0D3E9D4_A0A0D3E9D4_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A194W049_A0A194W049_9PEZI_105487 and tr_A0A194UVK3_A0A194UVK3_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A1S3YL66_A0A1S3YL66_TOBAC_4097 and tr_A0A1U7YBG2_A0A1U7YBG2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2H3BEH7_A0A2H3BEH7_9AGAR_1076256 and tr_A0A284R5N2_A0A284R5N2_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2K5LVA4_A0A2K5LVA4_CERAT_9531 and tr_A0A2K5ZQ89_A0A2K5ZQ89_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 45 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/P54868/4_raxmlng_ancestral/P54868.raxml.reduced.phy Alignment comprises 1 partitions and 508 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 508 Gaps: 11.52 % Invariant sites: 2.76 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54868/4_raxmlng_ancestral/P54868.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/P54868/3_mltree/P54868.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 127 / 10160 [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: -179119.406016 [00:00:00 -179119.406016] Initial branch length optimization [00:00:02 -178846.501114] Model parameter optimization (eps = 0.100000) [00:00:23] Tree #1, final logLikelihood: -178840.996060 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.210735,0.134573) (0.306926,0.468465) (0.222537,0.982618) (0.259802,2.344817) 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/P54868/4_raxmlng_ancestral/P54868.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54868/4_raxmlng_ancestral/P54868.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54868/4_raxmlng_ancestral/P54868.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54868/4_raxmlng_ancestral/P54868.raxml.log Analysis started: 03-Jun-2021 02:46:29 / finished: 03-Jun-2021 02:46:59 Elapsed time: 29.827 seconds Consumed energy: 1.342 Wh