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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 03-Jun-2021 14:56:07 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NQ38/2_msa/Q9NQ38_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NQ38/3_mltree/Q9NQ38.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NQ38/4_raxmlng_ancestral/Q9NQ38 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622721367 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/020621_run/phylogeny-snakemake/results/Q9NQ38/2_msa/Q9NQ38_nogap_msa.fasta [00:00:00] Loaded alignment with 397 taxa and 1064 sites WARNING: Sequences tr_A0A2I2Y2S6_A0A2I2Y2S6_GORGO_9595 and tr_H2RI08_H2RI08_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y2S6_A0A2I2Y2S6_GORGO_9595 and tr_A0A2R9BWI8_A0A2R9BWI8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QG31_G3QG31_GORGO_9595 and tr_H2QRR1_H2QRR1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QG31_G3QG31_GORGO_9595 and sp_P58062_ISK7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QG31_G3QG31_GORGO_9595 and tr_A0A2R9BGH2_A0A2R9BGH2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QZB2_G3QZB2_GORGO_9595 and tr_H2PGZ4_H2PGZ4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QZB2_G3QZB2_GORGO_9595 and sp_P00995_ISK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_W5P305_W5P305_SHEEP_9940 and tr_E1BNB0_E1BNB0_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q6IE38_ISK14_HUMAN_9606 and tr_A0A2R9CGE4_A0A2R9CGE4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7CPW6_F7CPW6_MACMU_9544 and tr_G7P8M3_G7P8M3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HE31_F7HE31_MACMU_9544 and tr_G7P8L5_G7P8L5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HE31_F7HE31_MACMU_9544 and tr_A0A096NAT0_A0A096NAT0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HE31_F7HE31_MACMU_9544 and tr_A0A2K5NJ41_A0A2K5NJ41_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HE31_F7HE31_MACMU_9544 and tr_A0A2K6D3G8_A0A2K6D3G8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HE31_F7HE31_MACMU_9544 and tr_A0A2K5ZTE8_A0A2K5ZTE8_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YQM5_H0YQM5_TAEGU_59729 and tr_A0A091F0W3_A0A091F0W3_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YQM5_H0YQM5_TAEGU_59729 and tr_A0A093GMH1_A0A093GMH1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_F1SE75_F1SE75_PIG_9823 and sp_P37109_ISK4_PIG_9823 are exactly identical! WARNING: Sequences tr_G7P8M4_G7P8M4_MACFA_9541 and tr_A0A0D9RHL1_A0A0D9RHL1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_W2R3K2_W2R3K2_PHYPN_761204 and tr_A0A0W8C364_A0A0W8C364_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R421_W2R421_PHYPN_761204 and tr_A0A0W8CJD5_A0A0W8CJD5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R421_W2R421_PHYPN_761204 and tr_W2KTE5_W2KTE5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A096NRL0_A0A096NRL0_PAPAN_9555 and tr_A0A0D9RHL5_A0A0D9RHL5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NY95_A0A096NY95_PAPAN_9555 and tr_A0A2K5NNJ5_A0A2K5NNJ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091JDN2_A0A091JDN2_EGRGA_188379 and tr_A0A099ZZ93_A0A099ZZ93_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087RD89_A0A087RD89_APTFO_9233 and tr_A0A099ZWG8_A0A099ZWG8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V0SEL9_A0A0V0SEL9_9BILA_6336 and tr_A0A0V1CSS2_A0A0V1CSS2_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0SEL9_A0A0V0SEL9_9BILA_6336 and tr_A0A0V0X1J7_A0A0V0X1J7_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0SEL9_A0A0V0SEL9_9BILA_6336 and tr_A0A0V0VQX4_A0A0V0VQX4_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0SEL9_A0A0V0SEL9_9BILA_6336 and tr_A0A0V1L3R8_A0A0V1L3R8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0SEL9_A0A0V0SEL9_9BILA_6336 and tr_A0A0V1PH58_A0A0V1PH58_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0SEL9_A0A0V0SEL9_9BILA_6336 and tr_A0A0V0TW96_A0A0V0TW96_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WXQ6_A0A0V0WXQ6_9BILA_92179 and tr_A0A0V1L2Q6_A0A0V1L2Q6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A2K5LPM1_A0A2K5LPM1_CERAT_9531 and tr_A0A2K5XHQ1_A0A2K5XHQ1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3V8Y5_A0A2U3V8Y5_TURTR_9739 and tr_A0A2Y9PGC1_A0A2Y9PGC1_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 35 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NQ38/4_raxmlng_ancestral/Q9NQ38.raxml.reduced.phy Alignment comprises 1 partitions and 1064 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1064 Gaps: 80.34 % Invariant sites: 4.70 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NQ38/4_raxmlng_ancestral/Q9NQ38.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/020621_run/phylogeny-snakemake/results/Q9NQ38/3_mltree/Q9NQ38.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 266 / 21280 [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: -64559.221572 [00:00:00 -64559.221572] Initial branch length optimization [00:00:00 -61805.962294] Model parameter optimization (eps = 0.100000) [00:01:20] Tree #1, final logLikelihood: -61487.832282 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.124031,0.252184) (0.058321,0.438894) (0.443161,0.826980) (0.374488,1.539808) 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/020621_run/phylogeny-snakemake/results/Q9NQ38/4_raxmlng_ancestral/Q9NQ38.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NQ38/4_raxmlng_ancestral/Q9NQ38.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NQ38/4_raxmlng_ancestral/Q9NQ38.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9NQ38/4_raxmlng_ancestral/Q9NQ38.raxml.log Analysis started: 03-Jun-2021 14:56:07 / finished: 03-Jun-2021 14:57:32 Elapsed time: 85.021 seconds Consumed energy: 4.560 Wh