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 02-Jun-2021 23:43:55 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZU5/2_msa/Q9GZU5_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZU5/3_mltree/Q9GZU5.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZU5/4_raxmlng_ancestral/Q9GZU5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622666635 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_020621/phylogeny-snakemake/results/Q9GZU5/2_msa/Q9GZU5_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 481 sites WARNING: Sequences tr_M3YZ90_M3YZ90_MUSPF_9669 and tr_A0A337S3C4_A0A337S3C4_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1RTQ5_G1RTQ5_NOMLE_61853 and tr_A0A2I3T1U4_A0A2I3T1U4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RTQ5_G1RTQ5_NOMLE_61853 and sp_O75093_SLIT1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RTQ5_G1RTQ5_NOMLE_61853 and tr_A0A2R8ZSB7_A0A2R8ZSB7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZDA6_A0A2I2ZDA6_GORGO_9595 and tr_A0A2I3RBH3_A0A2I3RBH3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QTA6_G3QTA6_GORGO_9595 and sp_Q9BZR6_RTN4R_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PZZ8_H2PZZ8_PANTR_9598 and tr_A0A2R8ZGF9_A0A2R8ZGF9_PANPA_9597 are exactly identical! WARNING: Sequences tr_B0XF31_B0XF31_CULQU_7176 and tr_B0XKB5_B0XKB5_CULQU_7176 are exactly identical! WARNING: Sequences tr_A0A1D5QW80_A0A1D5QW80_MACMU_9544 and tr_A0A0A0MUQ4_A0A0A0MUQ4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QW80_A0A1D5QW80_MACMU_9544 and tr_A0A0D9SAW2_A0A0D9SAW2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QW80_A0A1D5QW80_MACMU_9544 and tr_A0A2K5KYU3_A0A2K5KYU3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QW80_A0A1D5QW80_MACMU_9544 and tr_A0A2K6B317_A0A2K6B317_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7CX22_F7CX22_MACMU_9544 and tr_A0A2K6BN20_A0A2K6BN20_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H9D3_F7H9D3_MACMU_9544 and tr_A0A2I3M603_A0A2I3M603_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H9D3_F7H9D3_MACMU_9544 and tr_A0A2K5P0G9_A0A2K5P0G9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H9D3_F7H9D3_MACMU_9544 and tr_A0A2K6DXW7_A0A2K6DXW7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H9D3_F7H9D3_MACMU_9544 and tr_A0A2K5XKL1_A0A2K5XKL1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7NTT7_G7NTT7_MACFA_9541 and tr_A0A2K6B798_A0A2K6B798_MACNE_9545 are exactly identical! WARNING: Sequences tr_F1MYE4_F1MYE4_BOVIN_9913 and sp_Q27972_CHAD_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A087X6G4_A0A087X6G4_POEFO_48698 and tr_A0A087XER4_A0A087XER4_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A096MVL6_A0A096MVL6_PAPAN_9555 and tr_A0A2K5N6I2_A0A2K5N6I2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MVL6_A0A096MVL6_PAPAN_9555 and tr_A0A2K5Y3N5_A0A2K5Y3N5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NDP7_A0A096NDP7_PAPAN_9555 and tr_A0A2K5L1R7_A0A2K5L1R7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NDP7_A0A096NDP7_PAPAN_9555 and tr_A0A2K5X9U0_A0A2K5X9U0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9QYT5_A0A0D9QYT5_CHLSB_60711 and tr_A0A2K5MDJ4_A0A2K5MDJ4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RNT1_A0A0D9RNT1_CHLSB_60711 and tr_A0A2K6BUX2_A0A2K6BUX2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A226NEZ6_A0A226NEZ6_CALSU_9009 and tr_A0A226PAG5_A0A226PAG5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4ASP4_A0A2U4ASP4_TURTR_9739 and tr_A0A2Y9MKI2_A0A2Y9MKI2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3WKC2_A0A2U3WKC2_ODORO_9708 and tr_A0A2U3XAX6_A0A2U3XAX6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3WZR1_A0A2U3WZR1_ODORO_9708 and tr_A0A2Y9JUW0_A0A2Y9JUW0_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 30 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZU5/4_raxmlng_ancestral/Q9GZU5.raxml.reduced.phy Alignment comprises 1 partitions and 481 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 481 Gaps: 26.00 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZU5/4_raxmlng_ancestral/Q9GZU5.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_020621/phylogeny-snakemake/results/Q9GZU5/3_mltree/Q9GZU5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 121 / 9680 [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: -229627.072054 [00:00:00 -229627.072054] Initial branch length optimization [00:00:01 -225351.495584] Model parameter optimization (eps = 0.100000) [00:00:55] Tree #1, final logLikelihood: -223795.758876 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.160157,0.422479) (0.104858,0.389243) (0.455430,1.053683) (0.279555,1.472494) 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_020621/phylogeny-snakemake/results/Q9GZU5/4_raxmlng_ancestral/Q9GZU5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZU5/4_raxmlng_ancestral/Q9GZU5.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZU5/4_raxmlng_ancestral/Q9GZU5.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9GZU5/4_raxmlng_ancestral/Q9GZU5.raxml.log Analysis started: 02-Jun-2021 23:43:55 / finished: 02-Jun-2021 23:44:55 Elapsed time: 60.262 seconds