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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 12-Jul-2021 18:02:34 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P17039/2_msa/P17039_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P17039/3_mltree/P17039.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P17039/4_raxmlng_ancestral/P17039 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102154 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/P17039/2_msa/P17039_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 623 sites WARNING: Sequences tr_M3Y279_M3Y279_MUSPF_9669 and tr_A0A2Y9L647_A0A2Y9L647_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3FTK3_A0A2I3FTK3_NOMLE_61853 and tr_A0A2I3RJ81_A0A2I3RJ81_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R6A1_G3R6A1_GORGO_9595 and sp_Q8N972_ZN709_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2J8SK65_A0A2J8SK65_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2I3T1I2_A0A2I3T1I2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2I3LH46_A0A2I3LH46_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2K5XY05_A0A2K5XY05_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2R9C8X5_A0A2R9C8X5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F1P9J5_F1P9J5_CANLF_9615 and sp_Q9XSR1_ZN252_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2J8QIB0_A0A2J8QIB0_PANTR_9598 and sp_Q5MCW4_ZN569_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q781_H2Q781_PANTR_9598 and sp_P51523_ZNF84_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q781_H2Q781_PANTR_9598 and tr_A0A2R8Z7P5_A0A2R8Z7P5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCC1_H2QCC1_PANTR_9598 and sp_Q9P2J8_ZN624_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QG67_H2QG67_PANTR_9598 and tr_G7PXE1_G7PXE1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XKK1_F6XKK1_MACMU_9544 and tr_A0A2I3N067_A0A2I3N067_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6ZAL5_F6ZAL5_MACMU_9544 and tr_A0A2K5NSA5_A0A2K5NSA5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6ZAL5_F6ZAL5_MACMU_9544 and tr_A0A2K5YEE6_A0A2K5YEE6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7DJD1_F7DJD1_MACMU_9544 and tr_G7PZ21_G7PZ21_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DJD1_F7DJD1_MACMU_9544 and tr_A0A2K5NBK9_A0A2K5NBK9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DJD1_F7DJD1_MACMU_9544 and tr_A0A2K6CU82_A0A2K6CU82_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FDN3_F7FDN3_MACMU_9544 and tr_A0A2K6BUI0_A0A2K6BUI0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FTJ3_F7FTJ3_MACMU_9544 and tr_A0A2K6CFR0_A0A2K6CFR0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FX09_F7FX09_MACMU_9544 and tr_A0A2K6B732_A0A2K6B732_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HIL3_F7HIL3_MACMU_9544 and tr_A0A2K6D0A2_A0A2K6D0A2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PJI5_G7PJI5_MACFA_9541 and tr_A0A2K6C5V9_A0A2K6C5V9_MACNE_9545 are exactly identical! WARNING: Sequences sp_A2VDQ7_ZN420_BOVIN_9913 and tr_F1MML9_F1MML9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096MYB7_A0A096MYB7_PAPAN_9555 and tr_A0A2K6AAT3_A0A2K6AAT3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MXE9_A0A0A0MXE9_PAPAN_9555 and tr_A0A2K5MEC2_A0A2K5MEC2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3N004_A0A2I3N004_PAPAN_9555 and tr_A0A2K5MS65_A0A2K5MS65_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3N004_A0A2I3N004_PAPAN_9555 and tr_A0A2K5ZW36_A0A2K5ZW36_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 30 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/P17039/4_raxmlng_ancestral/P17039.raxml.reduced.phy Alignment comprises 1 partitions and 623 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 623 Gaps: 15.61 % Invariant sites: 1.28 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P17039/4_raxmlng_ancestral/P17039.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/P17039/3_mltree/P17039.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 156 / 12480 [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: -278891.229367 [00:00:00 -278891.229367] Initial branch length optimization [00:00:01 -277043.362753] Model parameter optimization (eps = 0.100000) [00:00:38] Tree #1, final logLikelihood: -276618.230081 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.162715,0.182037) (0.148805,0.613651) (0.369832,0.743228) (0.318648,1.896123) 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/P17039/4_raxmlng_ancestral/P17039.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P17039/4_raxmlng_ancestral/P17039.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P17039/4_raxmlng_ancestral/P17039.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P17039/4_raxmlng_ancestral/P17039.raxml.log Analysis started: 12-Jul-2021 18:02:34 / finished: 12-Jul-2021 18:03:18 Elapsed time: 44.534 seconds Consumed energy: 3.556 Wh