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 17:28:50 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75030/2_msa/O75030_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75030/3_mltree/O75030.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75030/4_raxmlng_ancestral/O75030 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100130 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/O75030/2_msa/O75030_nogap_msa.fasta [00:00:00] Loaded alignment with 831 taxa and 526 sites WARNING: Sequences sp_Q64705_USF2_MOUSE_10090 and sp_Q63665_USF2_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YQ82_M3YQ82_MUSPF_9669 and tr_A0A2Y9JDZ6_A0A2Y9JDZ6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YQT2_M3YQT2_MUSPF_9669 and tr_A0A2Y9JRJ6_A0A2Y9JRJ6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1RJU4_G1RJU4_NOMLE_61853 and tr_A0A2R9BI19_A0A2R9BI19_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_G3QMW3_G3QMW3_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_A0A2J8VHQ4_A0A2J8VHQ4_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_K7BZZ6_K7BZZ6_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_A0A287CV93_A0A287CV93_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and sp_P22415_USF1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_U3FX38_U3FX38_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_A0A096N9M5_A0A096N9M5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_A0A1U7UFP6_A0A1U7UFP6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_A0A2K5KP75_A0A2K5KP75_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_A0A2K6C7J7_A0A2K6C7J7_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_A0A2K5ZKN7_A0A2K5ZKN7_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3Z956_M3Z956_NOMLE_61853 and tr_A0A2R9AIR1_A0A2R9AIR1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YS93_A0A2I2YS93_GORGO_9595 and sp_P19532_TFE3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B8P4X4_B8P4X4_POSPM_561896 and tr_A0A1X6MPE3_A0A1X6MPE3_9APHY_670580 are exactly identical! WARNING: Sequences tr_A0A1D5QUV2_A0A1D5QUV2_MACMU_9544 and tr_G7P2I1_G7P2I1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QUV2_A0A1D5QUV2_MACMU_9544 and tr_A0A2K6ALQ3_A0A2K6ALQ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UXQ5_F6UXQ5_MACMU_9544 and tr_A0A2K5MJT8_A0A2K5MJT8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_G7Q2P5_G7Q2P5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A0D9RKQ6_A0A0D9RKQ6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A2K5LC64_A0A2K5LC64_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A2K6CFN5_A0A2K6CFN5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A2K5ZD31_A0A2K5ZD31_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FXN6_F7FXN6_MACMU_9544 and tr_A0A096NI31_A0A096NI31_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FXN6_F7FXN6_MACMU_9544 and tr_A0A2K5LZY5_A0A2K5LZY5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FXN6_F7FXN6_MACMU_9544 and tr_A0A2K6CP29_A0A2K6CP29_MACNE_9545 are exactly identical! WARNING: Sequences tr_I0FUV2_I0FUV2_MACMU_9544 and tr_A0A337SGF3_A0A337SGF3_FELCA_9685 are exactly identical! WARNING: Sequences tr_G5BWJ1_G5BWJ1_HETGA_10181 and tr_A0A091CKD5_A0A091CKD5_FUKDA_885580 are exactly identical! WARNING: Sequences tr_F7FA74_F7FA74_CALJA_9483 and tr_A0A2I3M2E5_A0A2I3M2E5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NZ88_G7NZ88_MACFA_9541 and tr_A0A2K5ZRN7_A0A2K5ZRN7_MANLE_9568 are exactly identical! WARNING: Sequences sp_A4IFU7_TFEC_BOVIN_9913 and tr_F1ML66_F1ML66_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A0A1MH28_A0A0A1MH28_9FUNG_58291 and tr_A0A367KBH5_A0A367KBH5_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1PD74_A0A0A1PD74_9FUNG_58291 and tr_A0A367JNQ5_A0A367JNQ5_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091KDI0_A0A091KDI0_EGRGA_188379 and tr_A0A087RBZ2_A0A087RBZ2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A165D7J5_A0A165D7J5_EXIGL_1314781 and tr_A0A165IP52_A0A165IP52_EXIGL_1314781 are exactly identical! WARNING: Sequences tr_A0A226MIU8_A0A226MIU8_CALSU_9009 and tr_A0A226NQX8_A0A226NQX8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QYF8_A0A2D0QYF8_ICTPU_7998 and tr_A0A2D0QYQ1_A0A2D0QYQ1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYG2_A0A2D0QYG2_ICTPU_7998 and tr_A0A2D0R090_A0A2D0R090_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3X4F1_A0A2U3X4F1_ODORO_9708 and tr_A0A2Y9L605_A0A2Y9L605_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2U3XH54_A0A2U3XH54_LEPWE_9713 and tr_A0A383YR62_A0A383YR62_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9NU69_A0A2Y9NU69_DELLE_9749 and tr_A0A2Y9FDH8_A0A2Y9FDH8_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 44 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/O75030/4_raxmlng_ancestral/O75030.raxml.reduced.phy Alignment comprises 1 partitions and 526 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 526 Gaps: 41.83 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75030/4_raxmlng_ancestral/O75030.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/O75030/3_mltree/O75030.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 132 / 10560 [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: -243346.459835 [00:00:00 -243346.459835] Initial branch length optimization [00:00:01 -167760.288333] Model parameter optimization (eps = 0.100000) [00:01:07] Tree #1, final logLikelihood: -167134.003762 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.088631,0.286434) (0.107640,1.270707) (0.357158,0.682936) (0.446572,1.329951) 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/O75030/4_raxmlng_ancestral/O75030.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75030/4_raxmlng_ancestral/O75030.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75030/4_raxmlng_ancestral/O75030.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75030/4_raxmlng_ancestral/O75030.raxml.log Analysis started: 12-Jul-2021 17:28:50 / finished: 12-Jul-2021 17:30:01 Elapsed time: 71.171 seconds Consumed energy: 6.119 Wh