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 14:20:46 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99728/2_msa/Q99728_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99728/3_mltree/Q99728.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99728/4_raxmlng_ancestral/Q99728 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805646 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/Q99728/2_msa/Q99728_nogap_msa.fasta [00:00:00] Loaded alignment with 992 taxa and 777 sites WARNING: Sequences tr_M3ZAS3_M3ZAS3_NOMLE_61853 and tr_A0A2R9BZG6_A0A2R9BZG6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R2V0_G3R2V0_GORGO_9595 and tr_H2Q295_H2Q295_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R2V0_G3R2V0_GORGO_9595 and sp_Q9H2K2_TNKS2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SDW9_G3SDW9_GORGO_9595 and tr_H2NVV6_H2NVV6_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SDW9_G3SDW9_GORGO_9595 and tr_K7CPS3_K7CPS3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SDW9_G3SDW9_GORGO_9595 and tr_A0A096N7Y0_A0A096N7Y0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3SDW9_G3SDW9_GORGO_9595 and tr_A0A2K5Z7H5_A0A2K5Z7H5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3SDW9_G3SDW9_GORGO_9595 and tr_A0A2R9ABR7_A0A2R9ABR7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NRT8_H2NRT8_PONAB_9601 and sp_Q6UB99_ANR11_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NRT8_H2NRT8_PONAB_9601 and tr_A0A2R9AHV0_A0A2R9AHV0_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q2M112_Q2M112_DROPS_46245 and tr_B4GQT7_B4GQT7_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A088ADB5_A0A088ADB5_APIME_7460 and tr_A0A2A3EDN9_A0A2A3EDN9_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A0E0GGR7_A0A0E0GGR7_ORYNI_4536 and tr_B8ANB1_B8ANB1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GGR7_A0A0E0GGR7_ORYNI_4536 and tr_A0A0E0NPM7_A0A0E0NPM7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H340_A0A0E0H340_ORYNI_4536 and tr_I1PMZ4_I1PMZ4_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0H340_A0A0E0H340_ORYNI_4536 and tr_A0A0E0PBI1_A0A0E0PBI1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H340_A0A0E0H340_ORYNI_4536 and tr_A0A0D3FXW0_A0A0D3FXW0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0H340_A0A0E0H340_ORYNI_4536 and tr_A0A0D9ZN34_A0A0D9ZN34_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A1D5Q2F7_A0A1D5Q2F7_MACMU_9544 and tr_A0A2K5ZIY5_A0A2K5ZIY5_MANLE_9568 are exactly identical! WARNING: Sequences tr_B8ARQ8_B8ARQ8_ORYSI_39946 and tr_Q7XPZ2_Q7XPZ2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1P7I9_I1P7I9_ORYGL_4538 and tr_A0A0D3FDR6_A0A0D3FDR6_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_M4ELY2_M4ELY2_BRARP_51351 and tr_A0A078ITX9_A0A078ITX9_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A096MZ63_A0A096MZ63_PAPAN_9555 and tr_A0A2K5XYL5_A0A2K5XYL5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P5H6_A0A096P5H6_PAPAN_9555 and tr_A0A0D9R2P6_A0A0D9R2P6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P5H6_A0A096P5H6_PAPAN_9555 and tr_A0A2K6CP90_A0A2K6CP90_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A078HXX2_A0A078HXX2_BRANA_3708 and tr_A0A0D3CLK5_A0A0D3CLK5_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A091EZN0_A0A091EZN0_CORBR_85066 and tr_A0A093SN16_A0A093SN16_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091EZN0_A0A091EZN0_CORBR_85066 and tr_A0A0A0ASG2_A0A0A0ASG2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091UK00_A0A091UK00_NIPNI_128390 and tr_A0A087QZ30_A0A087QZ30_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A087QQ48_A0A087QQ48_APTFO_9233 and tr_A0A091XEA7_A0A091XEA7_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A2I0LLX1_A0A2I0LLX1_COLLI_8932 and tr_A0A1V4K1J4_A0A1V4K1J4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A093GU87_A0A093GU87_DRYPU_118200 and tr_A0A091HIF2_A0A091HIF2_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1CIC8_A0A0V1CIC8_TRIBR_45882 and tr_A0A0V0UVE3_A0A0V0UVE3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CIC8_A0A0V1CIC8_TRIBR_45882 and tr_A0A0V0TR74_A0A0V0TR74_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S4AUT7_A0A1S4AUT7_TOBAC_4097 and tr_A0A1U7XQM7_A0A1U7XQM7_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CJT4_A0A1S4CJT4_TOBAC_4097 and tr_A0A1U7XC39_A0A1U7XC39_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CNU9_A0A1S4CNU9_TOBAC_4097 and tr_A0A1U7X3B2_A0A1U7X3B2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A226NC66_A0A226NC66_CALSU_9009 and tr_A0A226PEB1_A0A226PEB1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PL67_A0A2D0PL67_ICTPU_7998 and tr_A0A2D0PLA3_A0A2D0PLA3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PL67_A0A2D0PL67_ICTPU_7998 and tr_A0A2D0PMY1_A0A2D0PMY1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q5P0_A0A2D0Q5P0_ICTPU_7998 and tr_A0A2D0Q6U2_A0A2D0Q6U2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4C0X5_A0A2U4C0X5_TURTR_9739 and tr_A0A2Y9MRS4_A0A2Y9MRS4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C0X5_A0A2U4C0X5_TURTR_9739 and tr_A0A2Y9SMP1_A0A2Y9SMP1_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9LBM1_A0A2Y9LBM1_DELLE_9749 and tr_A0A2Y9F494_A0A2Y9F494_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 44 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/Q99728/4_raxmlng_ancestral/Q99728.raxml.reduced.phy Alignment comprises 1 partitions and 777 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 777 Gaps: 43.66 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99728/4_raxmlng_ancestral/Q99728.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/Q99728/3_mltree/Q99728.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 195 / 15600 [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: -377834.557371 [00:00:00 -377834.557371] Initial branch length optimization [00:00:02 -332551.230924] Model parameter optimization (eps = 0.100000) [00:11:08] Tree #1, final logLikelihood: -331589.050280 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.057274,0.383869) (0.043493,0.291415) (0.326494,0.711012) (0.572739,1.280162) 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/Q99728/4_raxmlng_ancestral/Q99728.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99728/4_raxmlng_ancestral/Q99728.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99728/4_raxmlng_ancestral/Q99728.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q99728/4_raxmlng_ancestral/Q99728.raxml.log Analysis started: 04-Jun-2021 14:20:46 / finished: 04-Jun-2021 14:32:02 Elapsed time: 675.997 seconds