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 17:32:05 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15043/2_msa/Q15043_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15043/3_mltree/Q15043.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15043/4_raxmlng_ancestral/Q15043 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100325 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/Q15043/2_msa/Q15043_nogap_msa.fasta [00:00:00] Loaded alignment with 995 taxa and 492 sites WARNING: Sequences tr_M3XPX1_M3XPX1_MUSPF_9669 and tr_A0A2Y9J0Q2_A0A2Y9J0Q2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and tr_A0A2I2YX43_A0A2I2YX43_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and tr_A0A2J8WVN7_A0A2J8WVN7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and tr_A0A2I3T5U1_A0A2I3T5U1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and sp_Q9ULF5_S39AA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and tr_F6WDC7_F6WDC7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and tr_G7PL28_G7PL28_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and tr_A0A096N0A4_A0A096N0A4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and tr_A0A0D9RHV8_A0A0D9RHV8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and tr_A0A2K5KJ54_A0A2K5KJ54_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R502_G1R502_NOMLE_61853 and tr_A0A2K6CA44_A0A2K6CA44_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QK74_G3QK74_GORGO_9595 and tr_H2R2F5_H2R2F5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QK74_G3QK74_GORGO_9595 and sp_Q9C0K1_S39A8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q29N95_Q29N95_DROPS_46245 and tr_B4G828_B4G828_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2J8Q1N0_A0A2J8Q1N0_PANTR_9598 and tr_A0A2R9CDT9_A0A2R9CDT9_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7CJL9_K7CJL9_PANTR_9598 and sp_Q92504_S39A7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CJL9_K7CJL9_PANTR_9598 and tr_A0A2R8ZZI2_A0A2R8ZZI2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NA85_A0A158NA85_ATTCE_12957 and tr_A0A195BKP4_A0A195BKP4_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6ZQI3_F6ZQI3_MACMU_9544 and tr_A0A096MUA8_A0A096MUA8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6ZQI3_F6ZQI3_MACMU_9544 and tr_A0A0D9RZ98_A0A0D9RZ98_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6ZQI3_F6ZQI3_MACMU_9544 and tr_A0A2K6CGA2_A0A2K6CGA2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GXH0_F7GXH0_MACMU_9544 and tr_G7PEH0_G7PEH0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GXH0_F7GXH0_MACMU_9544 and tr_A0A096P3N0_A0A096P3N0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GXH0_F7GXH0_MACMU_9544 and tr_A0A2K6DS42_A0A2K6DS42_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HA72_F7HA72_MACMU_9544 and tr_G7P2S2_G7P2S2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HA72_F7HA72_MACMU_9544 and tr_A0A096NHG1_A0A096NHG1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HA72_F7HA72_MACMU_9544 and tr_A0A0D9RAY7_A0A0D9RAY7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HA72_F7HA72_MACMU_9544 and tr_A0A2K5L7X8_A0A2K5L7X8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HKH5_F7HKH5_MACMU_9544 and tr_A0A0D9QVM1_A0A0D9QVM1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HKH5_F7HKH5_MACMU_9544 and tr_A0A2K5N828_A0A2K5N828_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HKH5_F7HKH5_MACMU_9544 and tr_A0A2K6B2Q1_A0A2K6B2Q1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0E0QK41_A0A0E0QK41_ORYRU_4529 and tr_A0A0E0AWE9_A0A0E0AWE9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A096MPW9_A0A096MPW9_PAPAN_9555 and tr_A0A2K6AEP0_A0A2K6AEP0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2D0R477_A0A2D0R477_ICTPU_7998 and tr_A0A2D0R498_A0A2D0R498_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R477_A0A2D0R477_ICTPU_7998 and tr_A0A2D0R5R9_A0A2D0R5R9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R477_A0A2D0R477_ICTPU_7998 and tr_A0A2D0R5S9_A0A2D0R5S9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R477_A0A2D0R477_ICTPU_7998 and tr_A0A2D0R6G6_A0A2D0R6G6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4BNL3_A0A2U4BNL3_TURTR_9739 and tr_A0A2Y9MVE1_A0A2Y9MVE1_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3W879_A0A2U3W879_ODORO_9708 and tr_A0A2U3YDJ3_A0A2U3YDJ3_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 39 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/Q15043/4_raxmlng_ancestral/Q15043.raxml.reduced.phy Alignment comprises 1 partitions and 492 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 492 Gaps: 30.28 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15043/4_raxmlng_ancestral/Q15043.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/Q15043/3_mltree/Q15043.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 123 / 9840 [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: -285057.281927 [00:00:00 -285057.281927] Initial branch length optimization [00:00:01 -216665.478547] Model parameter optimization (eps = 0.100000) [00:00:47] Tree #1, final logLikelihood: -215869.828107 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.162854,0.283245) (0.197311,0.415886) (0.314239,0.814877) (0.325597,1.891137) 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/Q15043/4_raxmlng_ancestral/Q15043.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15043/4_raxmlng_ancestral/Q15043.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15043/4_raxmlng_ancestral/Q15043.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15043/4_raxmlng_ancestral/Q15043.raxml.log Analysis started: 12-Jul-2021 17:32:05 / finished: 12-Jul-2021 17:32:58 Elapsed time: 52.698 seconds Consumed energy: 3.552 Wh