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 15-Jul-2021 14:45:17 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WVM7/2_msa/Q8WVM7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WVM7/3_mltree/Q8WVM7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WVM7/4_raxmlng_ancestral/Q8WVM7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626349517 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/Q8WVM7/2_msa/Q8WVM7_nogap_msa.fasta [00:00:00] Loaded alignment with 574 taxa and 1258 sites WARNING: Sequences tr_M3XQI7_M3XQI7_MUSPF_9669 and tr_A0A2Y9KJZ6_A0A2Y9KJZ6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3HJY3_A0A2I3HJY3_NOMLE_61853 and tr_G3QND0_G3QND0_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HJY3_A0A2I3HJY3_NOMLE_61853 and tr_K7CCP7_K7CCP7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HJY3_A0A2I3HJY3_NOMLE_61853 and tr_A0A2R9BTK7_A0A2R9BTK7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YS46_A0A2I2YS46_GORGO_9595 and sp_Q8WVM7_STAG1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YS46_A0A2I2YS46_GORGO_9595 and tr_H9EMJ5_H9EMJ5_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2YS46_A0A2I2YS46_GORGO_9595 and tr_G7NXX5_G7NXX5_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2YS46_A0A2I2YS46_GORGO_9595 and tr_A0A2I3LGJ8_A0A2I3LGJ8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2YS46_A0A2I2YS46_GORGO_9595 and tr_A0A2K6BMT6_A0A2K6BMT6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2YS46_A0A2I2YS46_GORGO_9595 and tr_A0A2K5YCP0_A0A2K5YCP0_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2QUR8_H2QUR8_PANTR_9598 and tr_A0A2R9BTA1_A0A2R9BTA1_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5PDD5_W5PDD5_SHEEP_9940 and tr_F1SL71_F1SL71_PIG_9823 are exactly identical! WARNING: Sequences tr_W5PDD5_W5PDD5_SHEEP_9940 and tr_F1MC39_F1MC39_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5PDD5_W5PDD5_SHEEP_9940 and tr_A0A2Y9EJ28_A0A2Y9EJ28_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5PDD5_W5PDD5_SHEEP_9940 and tr_A0A383Z6C3_A0A383Z6C3_BALAS_310752 are exactly identical! WARNING: Sequences tr_F1RU62_F1RU62_PIG_9823 and tr_A0A2U3UZH9_A0A2U3UZH9_TURTR_9739 are exactly identical! WARNING: Sequences tr_F1RU62_F1RU62_PIG_9823 and tr_A0A2Y9M775_A0A2Y9M775_DELLE_9749 are exactly identical! WARNING: Sequences tr_F1RU62_F1RU62_PIG_9823 and tr_A0A2Y9EY35_A0A2Y9EY35_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G7Q3M4_G7Q3M4_MACFA_9541 and tr_A0A0D9S0F3_A0A0D9S0F3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7Q3M4_G7Q3M4_MACFA_9541 and tr_A0A2K5LBQ4_A0A2K5LBQ4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7Q3M4_G7Q3M4_MACFA_9541 and tr_A0A2K6CBH6_A0A2K6CBH6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7Q3M4_G7Q3M4_MACFA_9541 and tr_A0A2K5Z7A0_A0A2K5Z7A0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151NNM6_A0A151NNM6_ALLMI_8496 and tr_A0A1U7RJM5_A0A1U7RJM5_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091IWD9_A0A091IWD9_EGRGA_188379 and tr_A0A099YX04_A0A099YX04_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A2D0QJR4_A0A2D0QJR4_ICTPU_7998 and tr_W5UCR7_W5UCR7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4B9D3_A0A2U4B9D3_TURTR_9739 and tr_A0A2Y9NZ72_A0A2Y9NZ72_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3WZC5_A0A2U3WZC5_ODORO_9708 and tr_A0A2U3X907_A0A2U3X907_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3WZC5_A0A2U3WZC5_ODORO_9708 and tr_A0A384DI60_A0A384DI60_URSMA_29073 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/300621_run/phylogeny-snakemake/results/Q8WVM7/4_raxmlng_ancestral/Q8WVM7.raxml.reduced.phy Alignment comprises 1 partitions and 1258 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1258 Gaps: 22.77 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WVM7/4_raxmlng_ancestral/Q8WVM7.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/Q8WVM7/3_mltree/Q8WVM7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 315 / 25200 [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: -254028.003558 [00:00:00 -254028.003558] Initial branch length optimization [00:00:01 -252925.744631] Model parameter optimization (eps = 0.100000) [00:00:37] Tree #1, final logLikelihood: -251991.970972 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.165665,0.435625) (0.138326,0.474017) (0.333575,0.734497) (0.362435,1.703076) 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/Q8WVM7/4_raxmlng_ancestral/Q8WVM7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WVM7/4_raxmlng_ancestral/Q8WVM7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WVM7/4_raxmlng_ancestral/Q8WVM7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8WVM7/4_raxmlng_ancestral/Q8WVM7.raxml.log Analysis started: 15-Jul-2021 14:45:17 / finished: 15-Jul-2021 14:46:02 Elapsed time: 44.745 seconds Consumed energy: 3.509 Wh