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 17:26:57 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/2_msa/Q70Z35_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/3_mltree/Q70Z35.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/4_raxmlng_ancestral/Q70Z35 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100017 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/Q70Z35/2_msa/Q70Z35_nogap_msa.fasta [00:00:00] Loaded alignment with 995 taxa and 1606 sites WARNING: Sequences tr_A0A1D5PL02_A0A1D5PL02_CHICK_9031 and tr_A0A226N1X1_A0A226N1X1_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q3UTH8_ARHG9_MOUSE_10090 and tr_A0A1U8CBG9_A0A1U8CBG9_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q7TNR9_ARHG4_MOUSE_10090 and tr_D3ZKB4_D3ZKB4_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XNJ2_M3XNJ2_MUSPF_9669 and tr_A0A2Y9L3R5_A0A2Y9L3R5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3QP24_G3QP24_GORGO_9595 and tr_H2QWM8_H2QWM8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QP24_G3QP24_GORGO_9595 and sp_Q8TB45_DPTOR_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QP24_G3QP24_GORGO_9595 and tr_F7BCX8_F7BCX8_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QP24_G3QP24_GORGO_9595 and tr_G1L5X3_G1L5X3_AILME_9646 are exactly identical! WARNING: Sequences tr_G3QP24_G3QP24_GORGO_9595 and tr_M3WE84_M3WE84_FELCA_9685 are exactly identical! WARNING: Sequences tr_G3QP24_G3QP24_GORGO_9595 and tr_A0A0D9RED8_A0A0D9RED8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QP24_G3QP24_GORGO_9595 and tr_A0A2R9BYL3_A0A2R9BYL3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QP24_G3QP24_GORGO_9595 and tr_A0A2Y9JAE7_A0A2Y9JAE7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3TQA2_A0A2I3TQA2_PANTR_9598 and tr_A0A2R8ZLA9_A0A2R8ZLA9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R6W0_H2R6W0_PANTR_9598 and tr_A0A2R9BZW5_A0A2R9BZW5_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BJ16_K7BJ16_PANTR_9598 and tr_A0A2R9BI86_A0A2R9BI86_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7DVN5_F7DVN5_HORSE_9796 and tr_G1L052_G1L052_AILME_9646 are exactly identical! WARNING: Sequences tr_F7DVN5_F7DVN5_HORSE_9796 and tr_A0A2I2UV85_A0A2I2UV85_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A3B5Q4B6_A0A3B5Q4B6_XIPMA_8083 and tr_A0A087XK17_A0A087XK17_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158P3R1_A0A158P3R1_ATTCE_12957 and tr_F4X211_F4X211_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158P3R1_A0A158P3R1_ATTCE_12957 and tr_A0A195BCT4_A0A195BCT4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158P3R1_A0A158P3R1_ATTCE_12957 and tr_A0A195F086_A0A195F086_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1D5Q1F9_A0A1D5Q1F9_MACMU_9544 and tr_A0A096NYR6_A0A096NYR6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q1F9_A0A1D5Q1F9_MACMU_9544 and tr_A0A2K6BFV7_A0A2K6BFV7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LP44_A0A2I3LP44_PAPAN_9555 and tr_A0A2K5NIF0_A0A2K5NIF0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LP44_A0A2I3LP44_PAPAN_9555 and tr_A0A2K6AMZ0_A0A2K6AMZ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LP44_A0A2I3LP44_PAPAN_9555 and tr_A0A2K5XW67_A0A2K5XW67_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091F9T3_A0A091F9T3_CORBR_85066 and tr_A0A093QBC7_A0A093QBC7_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091X471_A0A091X471_NIPNI_128390 and tr_A0A087QQS5_A0A087QQS5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091X471_A0A091X471_NIPNI_128390 and tr_A0A091WNE9_A0A091WNE9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091X471_A0A091X471_NIPNI_128390 and tr_A0A091H1D7_A0A091H1D7_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091X471_A0A091X471_NIPNI_128390 and tr_A0A0A0AJ58_A0A0A0AJ58_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091X471_A0A091X471_NIPNI_128390 and tr_A0A093GAT2_A0A093GAT2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A2I0MB49_A0A2I0MB49_COLLI_8932 and tr_A0A1V4KZC6_A0A1V4KZC6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2D0Q9N4_A0A2D0Q9N4_ICTPU_7998 and tr_W5UB82_W5UB82_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R9E4_A0A2D0R9E4_ICTPU_7998 and tr_A0A2D0RAL6_A0A2D0RAL6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SST6_A0A2D0SST6_ICTPU_7998 and tr_A0A2D0STC4_A0A2D0STC4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T6X3_A0A2D0T6X3_ICTPU_7998 and tr_A0A2D0T7M4_A0A2D0T7M4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KU83_A0A2K5KU83_CERAT_9531 and tr_A0A2K6B4N1_A0A2K6B4N1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5L4V7_A0A2K5L4V7_CERAT_9531 and tr_A0A2K5ZTJ0_A0A2K5ZTJ0_MANLE_9568 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/Q70Z35/4_raxmlng_ancestral/Q70Z35.raxml.reduced.phy Alignment comprises 1 partitions and 1606 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1606 Gaps: 59.22 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/4_raxmlng_ancestral/Q70Z35.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/Q70Z35/3_mltree/Q70Z35.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 402 / 32160 [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: -361313.253157 [00:00:00 -361313.253157] Initial branch length optimization [00:00:04 -321026.858063] Model parameter optimization (eps = 0.100000) [00:02:09] Tree #1, final logLikelihood: -319752.291544 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.088380,0.460235) (0.071072,0.589366) (0.449713,0.754861) (0.390835,1.478799) 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/Q70Z35/4_raxmlng_ancestral/Q70Z35.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/4_raxmlng_ancestral/Q70Z35.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/4_raxmlng_ancestral/Q70Z35.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/4_raxmlng_ancestral/Q70Z35.raxml.log Analysis started: 12-Jul-2021 17:26:57 / finished: 12-Jul-2021 17:29:21 Elapsed time: 144.391 seconds Consumed energy: 5.549 Wh