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 18:22:05 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P27986/2_msa/P27986_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P27986/3_mltree/P27986.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P27986/4_raxmlng_ancestral/P27986 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626103325 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/P27986/2_msa/P27986_nogap_msa.fasta [00:00:00] Loaded alignment with 983 taxa and 724 sites WARNING: Sequences tr_B4Q624_B4Q624_DROSI_7240 and tr_B4ICV4_B4ICV4_DROSE_7238 are exactly identical! WARNING: Sequences tr_Q8AYA6_Q8AYA6_CHICK_9031 and tr_A0A226MNK9_A0A226MNK9_CALSU_9009 are exactly identical! WARNING: Sequences tr_M3XLZ0_M3XLZ0_MUSPF_9669 and tr_A0A2Y9IT49_A0A2Y9IT49_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YTF0_M3YTF0_MUSPF_9669 and tr_A0A2Y9KPA9_A0A2Y9KPA9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3QTU7_G3QTU7_GORGO_9595 and tr_H2PDT8_H2PDT8_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QTU7_G3QTU7_GORGO_9595 and tr_A0A096MUE0_A0A096MUE0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QTU7_G3QTU7_GORGO_9595 and tr_A0A2K5MWD6_A0A2K5MWD6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R3V9_G3R3V9_GORGO_9595 and tr_H2Q6L9_H2Q6L9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RFQ2_G3RFQ2_GORGO_9595 and tr_K7DAA9_K7DAA9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RFQ2_G3RFQ2_GORGO_9595 and tr_A0A2R9BBY5_A0A2R9BBY5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2N7J9_H2N7J9_PONAB_9601 and tr_A0A2I3RH39_A0A2I3RH39_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N7J9_H2N7J9_PONAB_9601 and tr_A0A2R8ZHS7_A0A2R8ZHS7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TLP8_A0A2I3TLP8_PANTR_9598 and tr_A0A2R8ZV44_A0A2R8ZV44_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158ND87_A0A158ND87_ATTCE_12957 and tr_A0A195B1I2_A0A195B1I2_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NHS5_A0A158NHS5_ATTCE_12957 and tr_A0A195AX45_A0A195AX45_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6SBJ8_F6SBJ8_MACMU_9544 and tr_A0A096NMM0_A0A096NMM0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6UV94_F6UV94_MACMU_9544 and tr_A0A2K6AR12_A0A2K6AR12_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BZL6_F7BZL6_MACMU_9544 and tr_A0A096MNU6_A0A096MNU6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7BZL6_F7BZL6_MACMU_9544 and tr_A0A2K6A179_A0A2K6A179_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GRE8_F7GRE8_MACMU_9544 and tr_A0A096MNH2_A0A096MNH2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GRE8_F7GRE8_MACMU_9544 and tr_A0A0D9RT13_A0A0D9RT13_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GRE8_F7GRE8_MACMU_9544 and tr_A0A2K5MCJ8_A0A2K5MCJ8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GRE8_F7GRE8_MACMU_9544 and tr_A0A2K5ZRB2_A0A2K5ZRB2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6UMK3_F6UMK3_CALJA_9483 and tr_A0A383ZQN9_A0A383ZQN9_BALAS_310752 are exactly identical! WARNING: Sequences tr_V2XPN8_V2XPN8_MONRO_1381753 and tr_A0A0W0EV24_A0A0W0EV24_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A096MR68_A0A096MR68_PAPAN_9555 and tr_A0A0D9S7F0_A0A0D9S7F0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MR68_A0A096MR68_PAPAN_9555 and tr_A0A2K5MQ86_A0A2K5MQ86_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MR68_A0A096MR68_PAPAN_9555 and tr_A0A2K5ZT21_A0A2K5ZT21_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096MR68_A0A096MR68_PAPAN_9555 and tr_A0A2U3XCA0_A0A2U3XCA0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A0Q3R6H7_A0A0Q3R6H7_AMAAE_12930 and tr_A0A226PVG5_A0A226PVG5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A091W2L8_A0A091W2L8_NIPNI_128390 and tr_A0A087RBY7_A0A087RBY7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091W2L8_A0A091W2L8_NIPNI_128390 and tr_A0A091XQ08_A0A091XQ08_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091W2L8_A0A091W2L8_NIPNI_128390 and tr_A0A091GMV4_A0A091GMV4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0V1D3K6_A0A0V1D3K6_TRIBR_45882 and tr_A0A0V1PI33_A0A0V1PI33_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3HRF8_A0A1S3HRF8_LINUN_7574 and tr_A0A2R2MJ12_A0A2R2MJ12_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A2D0SCM0_A0A2D0SCM0_ICTPU_7998 and tr_A0A2D0SDZ1_A0A2D0SDZ1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V7D3_A0A2U3V7D3_TURTR_9739 and tr_A0A2Y9LEZ1_A0A2Y9LEZ1_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V7D3_A0A2U3V7D3_TURTR_9739 and tr_A0A2Y9SYH4_A0A2Y9SYH4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BK23_A0A2U4BK23_TURTR_9739 and tr_A0A2Y9NAQ0_A0A2Y9NAQ0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BK23_A0A2U4BK23_TURTR_9739 and tr_A0A383YPD9_A0A383YPD9_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4CGZ3_A0A2U4CGZ3_TURTR_9739 and tr_A0A2Y9NKL6_A0A2Y9NKL6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3XE97_A0A2U3XE97_LEPWE_9713 and tr_A0A384DBH2_A0A384DBH2_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 42 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/P27986/4_raxmlng_ancestral/P27986.raxml.reduced.phy Alignment comprises 1 partitions and 724 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 724 Gaps: 42.48 % Invariant sites: 0.14 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P27986/4_raxmlng_ancestral/P27986.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/P27986/3_mltree/P27986.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 181 / 14480 [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: -368409.428592 [00:00:00 -368409.428592] Initial branch length optimization [00:00:02 -255679.134000] Model parameter optimization (eps = 0.100000) [00:01:29] Tree #1, final logLikelihood: -253971.714733 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.122906,2.375310) (0.052192,0.160304) (0.398403,0.470328) (0.426498,1.201207) 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/P27986/4_raxmlng_ancestral/P27986.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P27986/4_raxmlng_ancestral/P27986.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P27986/4_raxmlng_ancestral/P27986.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P27986/4_raxmlng_ancestral/P27986.raxml.log Analysis started: 12-Jul-2021 18:22:05 / finished: 12-Jul-2021 18:23:41 Elapsed time: 95.784 seconds Consumed energy: 8.719 Wh