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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 14-Jul-2021 16:53:42 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/2_msa/Q6UXI7_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/3_mltree/Q6UXI7.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/4_raxmlng_ancestral/Q6UXI7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626270822 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/2_msa/Q6UXI7_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 678 sites WARNING: Sequences tr_A0A1D5NUG9_A0A1D5NUG9_CHICK_9031 and sp_P32018_COEA1_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A2I2YYV4_A0A2I2YYV4_GORGO_9595 and tr_A0A2J8QKY7_A0A2J8QKY7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YYV4_A0A2I2YYV4_GORGO_9595 and sp_O43405_COCH_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YYV4_A0A2I2YYV4_GORGO_9595 and tr_A0A2R9CAT6_A0A2R9CAT6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZDD6_A0A2I2ZDD6_GORGO_9595 and tr_K7BCL4_K7BCL4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZDD6_A0A2I2ZDD6_GORGO_9595 and tr_A0A2R9B2D4_A0A2R9B2D4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QJ50_G3QJ50_GORGO_9595 and sp_P12111_CO6A3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S125_G3S125_GORGO_9595 and tr_H2QTA4_H2QTA4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S125_G3S125_GORGO_9595 and sp_Q99715_COCA1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QT85_H2QT85_PANTR_9598 and tr_A0A2R9B2E7_A0A2R9B2E7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5RDG7_A0A1D5RDG7_MACMU_9544 and tr_A0A2K6B911_A0A2K6B911_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XMZ4_F6XMZ4_MACMU_9544 and tr_G7PA12_G7PA12_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XMZ4_F6XMZ4_MACMU_9544 and tr_A0A2K6BTQ0_A0A2K6BTQ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7AG99_F7AG99_MACMU_9544 and tr_A0A0D9R1F2_A0A0D9R1F2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7FYZ2_F7FYZ2_MACMU_9544 and tr_A0A096N2S0_A0A096N2S0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FYZ2_F7FYZ2_MACMU_9544 and tr_A0A2K6CSK8_A0A2K6CSK8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PCQ7_G7PCQ7_MACFA_9541 and tr_A0A2I3M793_A0A2I3M793_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PCQ7_G7PCQ7_MACFA_9541 and tr_A0A2K5KXA8_A0A2K5KXA8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PCQ7_G7PCQ7_MACFA_9541 and tr_A0A2K6CB99_A0A2K6CB99_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PCQ7_G7PCQ7_MACFA_9541 and tr_A0A2K5YVX9_A0A2K5YVX9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096N9M9_A0A096N9M9_PAPAN_9555 and tr_A0A2K5XYG8_A0A2K5XYG8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MEB4_A0A2I3MEB4_PAPAN_9555 and tr_A0A2K6A2G4_A0A2K6A2G4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9RNM7_A0A0D9RNM7_CHLSB_60711 and tr_A0A2K6DG14_A0A2K6DG14_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2D0Q1E0_A0A2D0Q1E0_ICTPU_7998 and tr_W5UM53_W5UM53_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEE3_A0A2D0QEE3_ICTPU_7998 and tr_A0A2D0QGY0_A0A2D0QGY0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEE3_A0A2D0QEE3_ICTPU_7998 and tr_A0A2D0QGY7_A0A2D0QGY7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEE3_A0A2D0QEE3_ICTPU_7998 and tr_A0A2D0QHS1_A0A2D0QHS1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEE9_A0A2D0QEE9_ICTPU_7998 and tr_A0A2D0QFH7_A0A2D0QFH7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QFI0_A0A2D0QFI0_ICTPU_7998 and tr_A0A2D0QGZ0_A0A2D0QGZ0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNL3_A0A2D0QNL3_ICTPU_7998 and tr_A0A2D0QP39_A0A2D0QP39_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNL3_A0A2D0QNL3_ICTPU_7998 and tr_A0A2D0QRG5_A0A2D0QRG5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R7E9_A0A2D0R7E9_ICTPU_7998 and tr_A0A2D0R7G8_A0A2D0R7G8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R7E9_A0A2D0R7E9_ICTPU_7998 and tr_A0A2D0R8Z6_A0A2D0R8Z6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5P5K0_A0A2K5P5K0_CERAT_9531 and tr_A0A2K5ZDS6_A0A2K5ZDS6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4C285_A0A2U4C285_TURTR_9739 and tr_A0A2U4C2C5_A0A2U4C2C5_TURTR_9739 are exactly identical! WARNING: Duplicate sequences found: 35 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/4_raxmlng_ancestral/Q6UXI7.raxml.reduced.phy Alignment comprises 1 partitions and 678 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 678 Gaps: 35.96 % Invariant sites: 0.15 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/4_raxmlng_ancestral/Q6UXI7.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/3_mltree/Q6UXI7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 170 / 13600 [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: -193801.226205 [00:00:00 -193801.226205] Initial branch length optimization [00:00:01 -187842.258863] Model parameter optimization (eps = 0.100000) [00:00:45] Tree #1, final logLikelihood: -187348.794426 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.093434,0.339943) (0.160221,0.386582) (0.320276,0.772416) (0.426070,1.546491) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/4_raxmlng_ancestral/Q6UXI7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/4_raxmlng_ancestral/Q6UXI7.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/4_raxmlng_ancestral/Q6UXI7.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/4_raxmlng_ancestral/Q6UXI7.raxml.log Analysis started: 14-Jul-2021 16:53:42 / finished: 14-Jul-2021 16:54:33 Elapsed time: 51.947 seconds