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 02-Jun-2021 18:33:14 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6R1/2_msa/Q9Y6R1_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6R1/3_mltree/Q9Y6R1.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6R1/4_raxmlng_ancestral/Q9Y6R1 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647994 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/Q9Y6R1/2_msa/Q9Y6R1_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1079 sites WARNING: Sequences tr_G3R9D5_G3R9D5_GORGO_9595 and tr_H2NHB6_H2NHB6_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R9D5_G3R9D5_GORGO_9595 and tr_H2Q5Y3_H2Q5Y3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R9D5_G3R9D5_GORGO_9595 and tr_A0A0D9R0P3_A0A0D9R0P3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R9D5_G3R9D5_GORGO_9595 and tr_A0A2K5M6F7_A0A2K5M6F7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R9D5_G3R9D5_GORGO_9595 and tr_A0A2R9AN33_A0A2R9AN33_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QJH6_H2QJH6_PANTR_9598 and sp_P48751_B3A3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QJH6_H2QJH6_PANTR_9598 and tr_A0A1D5QIC6_A0A1D5QIC6_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2QJH6_H2QJH6_PANTR_9598 and tr_A0A0D9R699_A0A0D9R699_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QDA6_A0A1D5QDA6_MACMU_9544 and tr_A0A2I3MYK2_A0A2I3MYK2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QDA6_A0A1D5QDA6_MACMU_9544 and tr_A0A2K5NZ98_A0A2K5NZ98_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FRN6_F7FRN6_MACMU_9544 and tr_G7P5M4_G7P5M4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MNG7_G7MNG7_MACMU_9544 and tr_A0A0D9R2Z3_A0A0D9R2Z3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MUV2_A0A096MUV2_PAPAN_9555 and tr_A0A2K5KJF4_A0A2K5KJF4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MUV2_A0A096MUV2_PAPAN_9555 and tr_A0A2K6AHU5_A0A2K6AHU5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9RSZ5_A0A0D9RSZ5_CHLSB_60711 and tr_A0A2K6CC84_A0A2K6CC84_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091J967_A0A091J967_EGRGA_188379 and tr_A0A091UUE6_A0A091UUE6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A0V1D3J5_A0A0V1D3J5_TRIBR_45882 and tr_A0A0V0WJI9_A0A0V0WJI9_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1D5J8_A0A0V1D5J8_TRIBR_45882 and tr_A0A0V0UGT8_A0A0V0UGT8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WGY1_A0A0V0WGY1_9BILA_92179 and tr_A0A0V1LEV4_A0A0V1LEV4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WRF1_A0A0V0WRF1_9BILA_92179 and tr_A0A0V1L882_A0A0V1L882_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0VSU7_A0A0V0VSU7_9BILA_181606 and tr_A0A0V1A4R3_A0A0V1A4R3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1L483_A0A0V1L483_9BILA_6335 and tr_A0A0V1A097_A0A0V1A097_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1L483_A0A0V1L483_9BILA_6335 and tr_A0A0V1P7M7_A0A0V1P7M7_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1L483_A0A0V1L483_9BILA_6335 and tr_A0A0V0TXT8_A0A0V0TXT8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1PN35_A0A0V1PN35_9BILA_92180 and tr_A0A0V0TZN1_A0A0V0TZN1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A2D0PNR4_A0A2D0PNR4_ICTPU_7998 and tr_W5ULC3_W5ULC3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RA90_A0A2D0RA90_ICTPU_7998 and tr_A0A2D0RA94_A0A2D0RA94_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SF59_A0A2D0SF59_ICTPU_7998 and tr_A0A2D0SFV8_A0A2D0SFV8_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 28 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/Q9Y6R1/4_raxmlng_ancestral/Q9Y6R1.raxml.reduced.phy Alignment comprises 1 partitions and 1079 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1079 Gaps: 14.92 % Invariant sites: 0.19 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6R1/4_raxmlng_ancestral/Q9Y6R1.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/Q9Y6R1/3_mltree/Q9Y6R1.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 270 / 21600 [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: -304389.109506 [00:00:00 -304389.109506] Initial branch length optimization [00:00:01 -304143.561221] Model parameter optimization (eps = 0.100000) [00:01:15] Tree #1, final logLikelihood: -302966.045568 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.246462,0.336833) (0.232069,0.501845) (0.303119,0.983783) (0.218351,2.300508) 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/Q9Y6R1/4_raxmlng_ancestral/Q9Y6R1.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6R1/4_raxmlng_ancestral/Q9Y6R1.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6R1/4_raxmlng_ancestral/Q9Y6R1.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6R1/4_raxmlng_ancestral/Q9Y6R1.raxml.log Analysis started: 02-Jun-2021 18:33:14 / finished: 02-Jun-2021 18:34:40 Elapsed time: 86.634 seconds Consumed energy: 5.032 Wh