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 12:35:33 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD19/2_msa/Q8TD19_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD19/3_mltree/Q8TD19.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD19/4_raxmlng_ancestral/Q8TD19 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626255333 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/Q8TD19/2_msa/Q8TD19_nogap_msa.fasta [00:00:00] Loaded alignment with 994 taxa and 979 sites WARNING: Sequences tr_Q5F3P1_Q5F3P1_CHICK_9031 and tr_H0Z1R3_H0Z1R3_TAEGU_59729 are exactly identical! WARNING: Sequences tr_Q5F3P1_Q5F3P1_CHICK_9031 and tr_U3JJB6_U3JJB6_FICAL_59894 are exactly identical! WARNING: Sequences tr_Q5F3P1_Q5F3P1_CHICK_9031 and tr_U3ILU9_U3ILU9_ANAPL_8839 are exactly identical! WARNING: Sequences tr_Q5F3P1_Q5F3P1_CHICK_9031 and tr_A0A0Q3Q1T8_A0A0Q3Q1T8_AMAAE_12930 are exactly identical! WARNING: Sequences tr_Q5F3P1_Q5F3P1_CHICK_9031 and tr_A0A093QAD4_A0A093QAD4_9PASS_328815 are exactly identical! WARNING: Sequences tr_Q5F3P1_Q5F3P1_CHICK_9031 and tr_A0A091VZU7_A0A091VZU7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_Q5F3P1_Q5F3P1_CHICK_9031 and tr_A0A087R9J0_A0A087R9J0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A2J8L8I7_A0A2J8L8I7_PANTR_9598 and sp_P51956_NEK3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q134_H2Q134_PANTR_9598 and tr_A0A2R9AXA8_A0A2R9AXA8_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q2U6P5_Q2U6P5_ASPOR_510516 and tr_A0A1S9D914_A0A1S9D914_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_F6U7G5_F6U7G5_MACMU_9544 and tr_A0A2K6D0N3_A0A2K6D0N3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UM89_F6UM89_MACMU_9544 and tr_G7PTY4_G7PTY4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6UM89_F6UM89_MACMU_9544 and tr_A0A2K5NPU5_A0A2K5NPU5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6UM89_F6UM89_MACMU_9544 and tr_A0A2K6DDI2_A0A2K6DDI2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UM89_F6UM89_MACMU_9544 and tr_A0A2K5XGK4_A0A2K5XGK4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7C8J4_F7C8J4_MACMU_9544 and tr_A0A096NPN1_A0A096NPN1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7C8J4_F7C8J4_MACMU_9544 and tr_A0A0D9RS67_A0A0D9RS67_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7C8J4_F7C8J4_MACMU_9544 and tr_A0A2K5KM94_A0A2K5KM94_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7C8J4_F7C8J4_MACMU_9544 and tr_A0A2K6AAM9_A0A2K6AAM9_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GZ09_F7GZ09_MACMU_9544 and tr_A0A0D9S233_A0A0D9S233_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GZ09_F7GZ09_MACMU_9544 and tr_A0A2K6DRZ8_A0A2K6DRZ8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F4NXH4_F4NXH4_BATDJ_684364 and tr_A0A177WJN8_A0A177WJN8_BATDE_403673 are exactly identical! WARNING: Sequences tr_W2QCT3_W2QCT3_PHYPN_761204 and tr_A0A0W8DF58_A0A0W8DF58_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QCT3_W2QCT3_PHYPN_761204 and tr_W2LCI1_W2LCI1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2R2J6_W2R2J6_PHYPN_761204 and tr_A0A0W8D357_A0A0W8D357_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R2J6_W2R2J6_PHYPN_761204 and tr_W2G8P3_W2G8P3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0F8V018_A0A0F8V018_9EURO_308745 and tr_A0A2T5LRH0_A0A2T5LRH0_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0G4NVY7_A0A0G4NVY7_PENCA_1429867 and tr_A0A1V6QZH3_A0A1V6QZH3_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A100IQU2_A0A100IQU2_ASPNG_5061 and tr_A0A1L9MT86_A0A1L9MT86_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A100IQU2_A0A100IQU2_ASPNG_5061 and tr_A0A317VNF1_A0A317VNF1_9EURO_1448314 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_300621/phylogeny-snakemake/results/Q8TD19/4_raxmlng_ancestral/Q8TD19.raxml.reduced.phy Alignment comprises 1 partitions and 979 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 979 Gaps: 47.76 % Invariant sites: 0.10 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD19/4_raxmlng_ancestral/Q8TD19.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/Q8TD19/3_mltree/Q8TD19.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 245 / 19600 [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: -393648.074240 [00:00:00 -393648.074240] Initial branch length optimization [00:00:02 -371837.826140] Model parameter optimization (eps = 0.100000) [00:01:05] Tree #1, final logLikelihood: -370589.015575 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.058219,0.179925) (0.093915,0.212880) (0.292963,0.734418) (0.554903,1.359473) 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/Q8TD19/4_raxmlng_ancestral/Q8TD19.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD19/4_raxmlng_ancestral/Q8TD19.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD19/4_raxmlng_ancestral/Q8TD19.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8TD19/4_raxmlng_ancestral/Q8TD19.raxml.log Analysis started: 14-Jul-2021 12:35:33 / finished: 14-Jul-2021 12:36:47 Elapsed time: 73.989 seconds