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 18:15:36 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRC6/2_msa/Q9NRC6_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRC6/3_mltree/Q9NRC6.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRC6/4_raxmlng_ancestral/Q9NRC6 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102936 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/Q9NRC6/2_msa/Q9NRC6_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 3674 sites WARNING: Sequences sp_Q9JI91_ACTN2_MOUSE_10090 and tr_D3ZCV0_D3ZCV0_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Y7F4_M3Y7F4_MUSPF_9669 and tr_A0A2Y9JK69_A0A2Y9JK69_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3GFP9_A0A2I3GFP9_NOMLE_61853 and tr_G3QSY2_G3QSY2_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GFP9_A0A2I3GFP9_NOMLE_61853 and tr_A0A2K6CB71_A0A2K6CB71_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D8JUP7_A0A0D8JUP7_COCIM_246410 and tr_E9DI27_E9DI27_COCPS_443226 are exactly identical! WARNING: Sequences tr_A0A0D8JUP7_A0A0D8JUP7_COCIM_246410 and tr_A0A0J6Y5M8_A0A0J6Y5M8_COCIT_404692 are exactly identical! WARNING: Sequences tr_E2QUQ0_E2QUQ0_CANLF_9615 and tr_G1L2Z4_G1L2Z4_AILME_9646 are exactly identical! WARNING: Sequences tr_E2QY08_E2QY08_CANLF_9615 and tr_A0A2U3ZCZ8_A0A2U3ZCZ8_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3STF2_A0A2I3STF2_PANTR_9598 and tr_A0A0A0MU58_A0A0A0MU58_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3STF2_A0A2I3STF2_PANTR_9598 and tr_A0A2K5LF87_A0A2K5LF87_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3STF2_A0A2I3STF2_PANTR_9598 and tr_A0A2R9C199_A0A2R9C199_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FB66_F9FB66_FUSOF_660025 and tr_A0A0D2XE00_A0A0D2XE00_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FB66_F9FB66_FUSOF_660025 and tr_X0D2U0_X0D2U0_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FB66_F9FB66_FUSOF_660025 and tr_A0A2H3TC30_A0A2H3TC30_FUSOX_5507 are exactly identical! WARNING: Sequences sp_O43707_ACTN4_HUMAN_9606 and tr_F7HU82_F7HU82_MACMU_9544 are exactly identical! WARNING: Sequences sp_O43707_ACTN4_HUMAN_9606 and tr_A0A0D9QVJ0_A0A0D9QVJ0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A0D9RKZ5_A0A0D9RKZ5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A2K5N6P5_A0A2K5N6P5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A2K6CYT7_A0A2K6CYT7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A2K5ZZ84_A0A2K5ZZ84_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6VRJ5_F6VRJ5_MACMU_9544 and tr_A0A2K5N9D6_A0A2K5N9D6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G2YIJ6_G2YIJ6_BOTF4_999810 and tr_M7UL09_M7UL09_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A0A059IXW0_A0A059IXW0_9EURO_1215338 and tr_A0A178F4W9_A0A178F4W9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A094EK08_A0A094EK08_9PEZI_1420912 and tr_A0A1B8GA32_A0A1B8GA32_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0D9RBH8_A0A0D9RBH8_CHLSB_60711 and tr_A0A2K6E8I1_A0A2K6E8I1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151MB02_A0A151MB02_ALLMI_8496 and tr_A0A1U7S444_A0A1U7S444_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091ITT8_A0A091ITT8_EGRGA_188379 and tr_A0A091VVI2_A0A091VVI2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091ITT8_A0A091ITT8_EGRGA_188379 and tr_A0A091VWV9_A0A091VWV9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091ITT8_A0A091ITT8_EGRGA_188379 and tr_A0A0A0ADT3_A0A0A0ADT3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A091UMG4_A0A091UMG4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A087R6Z3_A0A087R6Z3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A091G6Y8_A0A091G6Y8_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A0A0AHU9_A0A0A0AHU9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0MTN9_A0A2I0MTN9_COLLI_8932 and tr_A0A1V4JKI3_A0A1V4JKI3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CWE6_A0A0V1CWE6_TRIBR_45882 and tr_A0A0V0VNJ7_A0A0V0VNJ7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CWE6_A0A0V1CWE6_TRIBR_45882 and tr_A0A0V0ZNF3_A0A0V0ZNF3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CWE6_A0A0V1CWE6_TRIBR_45882 and tr_A0A0V0TZT7_A0A0V0TZT7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0X125_A0A0V0X125_9BILA_92179 and tr_A0A0V1KXT2_A0A0V1KXT2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A2D0RQD2_A0A2D0RQD2_ICTPU_7998 and tr_A0A2D0RR08_A0A2D0RR08_ICTPU_7998 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/Q9NRC6/4_raxmlng_ancestral/Q9NRC6.raxml.reduced.phy Alignment comprises 1 partitions and 3674 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 3674 Gaps: 67.62 % Invariant sites: 0.22 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRC6/4_raxmlng_ancestral/Q9NRC6.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/Q9NRC6/3_mltree/Q9NRC6.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 919 / 73520 [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: -595424.499698 [00:00:01 -595424.499698] Initial branch length optimization [00:00:07 -580197.780258] Model parameter optimization (eps = 0.100000) [00:02:05] Tree #1, final logLikelihood: -579386.550909 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.051763,0.094549) (0.124280,0.329136) (0.421303,0.690372) (0.402654,1.647431) 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/Q9NRC6/4_raxmlng_ancestral/Q9NRC6.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRC6/4_raxmlng_ancestral/Q9NRC6.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRC6/4_raxmlng_ancestral/Q9NRC6.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NRC6/4_raxmlng_ancestral/Q9NRC6.raxml.log Analysis started: 12-Jul-2021 18:15:36 / finished: 12-Jul-2021 18:18:16 Elapsed time: 160.109 seconds Consumed energy: 5.337 Wh