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 13:33:17 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10619/2_msa/P10619_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10619/3_mltree/P10619.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10619/4_raxmlng_ancestral/P10619 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802797 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/P10619/2_msa/P10619_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 480 sites WARNING: Sequences tr_A0A0E0GMH8_A0A0E0GMH8_ORYNI_4536 and tr_B8A7F9_B8A7F9_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GMH8_A0A0E0GMH8_ORYNI_4536 and tr_A0A0E0MVQ7_A0A0E0MVQ7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GMH8_A0A0E0GMH8_ORYNI_4536 and tr_Q5ZA19_Q5ZA19_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0GZ70_A0A0E0GZ70_ORYNI_4536 and tr_B8AS93_B8AS93_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GZ70_A0A0E0GZ70_ORYNI_4536 and tr_Q7X7Y5_Q7X7Y5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F7G1E1_F7G1E1_MACMU_9544 and tr_A0A2K5L7U4_A0A2K5L7U4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A2XSY0_A2XSY0_ORYSI_39946 and tr_I1P623_I1P623_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2XSY0_A2XSY0_ORYSI_39946 and tr_A0A0E0P8H2_A0A0E0P8H2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1NMT2_I1NMT2_ORYGL_4538 and tr_A0A0D3ENB9_A0A0D3ENB9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1NMT2_I1NMT2_ORYGL_4538 and tr_A0A0D9Y7T4_A0A0D9Y7T4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1Q052_I1Q052_ORYGL_4538 and tr_A0A0E0PUF2_A0A0E0PUF2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1Q052_I1Q052_ORYGL_4538 and tr_A0A0E0A603_A0A0E0A603_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_B3RZK7_B3RZK7_TRIAD_10228 and tr_A0A369RWS7_A0A369RWS7_9METZ_287889 are exactly identical! WARNING: Sequences tr_B3S4P4_B3S4P4_TRIAD_10228 and tr_A0A369SJ17_A0A369SJ17_9METZ_287889 are exactly identical! WARNING: Sequences tr_B3SBA1_B3SBA1_TRIAD_10228 and tr_A0A369RSW6_A0A369RSW6_9METZ_287889 are exactly identical! WARNING: Sequences tr_M4EV48_M4EV48_BRARP_51351 and tr_A0A078HQ25_A0A078HQ25_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4FDI4_M4FDI4_BRARP_51351 and tr_A0A078HL24_A0A078HL24_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2Q7F3_W2Q7F3_PHYPN_761204 and tr_A0A0W8D576_A0A0W8D576_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2Q889_W2Q889_PHYPN_761204 and tr_A0A0W8CLL4_A0A0W8CLL4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A2I3MIK9_A0A2I3MIK9_PAPAN_9555 and tr_A0A2K6D8B4_A0A2K6D8B4_MACNE_9545 are exactly identical! WARNING: Sequences tr_V4UEA9_V4UEA9_9ROSI_85681 and tr_A0A2H5N2H1_A0A2H5N2H1_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2TIP7_A0A0D2TIP7_GOSRA_29730 and tr_A0A1U8M9I2_A0A1U8M9I2_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2TTP0_A0A0D2TTP0_GOSRA_29730 and tr_A0A1U8KT94_A0A1U8KT94_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A1S4BYQ8_A0A1S4BYQ8_TOBAC_4097 and tr_A0A1U7X4N3_A0A1U7X4N3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CLQ3_A0A1S4CLQ3_TOBAC_4097 and tr_A0A1U7WX15_A0A1U7WX15_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CS57_A0A1S4CS57_TOBAC_4097 and tr_A0A1U7YE28_A0A1U7YE28_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DAV4_A0A1S4DAV4_TOBAC_4097 and tr_A0A1U7YA69_A0A1U7YA69_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DFX1_A0A1S4DFX1_TOBAC_4097 and tr_A0A1U7YMU5_A0A1U7YMU5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2U1MUA4_A0A2U1MUA4_ARTAN_35608 and tr_A0A2U1PYY7_A0A2U1PYY7_ARTAN_35608 are exactly identical! WARNING: Duplicate sequences found: 29 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/P10619/4_raxmlng_ancestral/P10619.raxml.reduced.phy Alignment comprises 1 partitions and 480 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 480 Gaps: 15.79 % Invariant sites: 0.42 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10619/4_raxmlng_ancestral/P10619.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/P10619/3_mltree/P10619.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 120 / 9600 [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: -261136.102443 [00:00:00 -261136.102443] Initial branch length optimization [00:00:01 -260750.462216] Model parameter optimization (eps = 0.100000) [00:00:31] Tree #1, final logLikelihood: -260466.162342 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.113593,0.156904) (0.244877,0.315371) (0.318788,0.886232) (0.322742,1.928567) 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/P10619/4_raxmlng_ancestral/P10619.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10619/4_raxmlng_ancestral/P10619.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10619/4_raxmlng_ancestral/P10619.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P10619/4_raxmlng_ancestral/P10619.raxml.log Analysis started: 04-Jun-2021 13:33:17 / finished: 04-Jun-2021 13:33:53 Elapsed time: 35.817 seconds