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 12-Jul-2021 17:52:59 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXX3/2_msa/Q9BXX3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXX3/3_mltree/Q9BXX3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXX3/4_raxmlng_ancestral/Q9BXX3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101579 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/Q9BXX3/2_msa/Q9BXX3_nogap_msa.fasta [00:00:00] Loaded alignment with 959 taxa and 1397 sites WARNING: Sequences tr_A0A1D5P3L8_A0A1D5P3L8_CHICK_9031 and tr_H0YTV7_H0YTV7_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1D5P3L8_A0A1D5P3L8_CHICK_9031 and tr_A0A091UIT4_A0A091UIT4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5P3L8_A0A1D5P3L8_CHICK_9031 and tr_A0A087R3L6_A0A087R3L6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5P3L8_A0A1D5P3L8_CHICK_9031 and tr_A0A091FS51_A0A091FS51_9AVES_55661 are exactly identical! WARNING: Sequences tr_E9Q637_E9Q637_MOUSE_10090 and tr_Q8C646_Q8C646_MOUSE_10090 are exactly identical! WARNING: Sequences tr_M3YAX0_M3YAX0_MUSPF_9669 and tr_A0A2Y9IKB6_A0A2Y9IKB6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_L5JUQ0_L5JUQ0_PTEAL_9402 are exactly identical! WARNING: Sequences tr_B8NQZ3_B8NQZ3_ASPFN_332952 and tr_A0A1S9DSF0_A0A1S9DSF0_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_F1PXC5_F1PXC5_CANLF_9615 and tr_A0A384DKR3_A0A384DKR3_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3SVD9_A0A2I3SVD9_PANTR_9598 and sp_Q92527_ANKR7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SVD9_A0A2I3SVD9_PANTR_9598 and tr_A0A2R8ZJB4_A0A2R8ZJB4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6UZC4_F6UZC4_MONDO_13616 and tr_A0A2Y9RIG2_A0A2Y9RIG2_TRIMA_127582 are exactly identical! WARNING: Sequences tr_F6W4W9_F6W4W9_HORSE_9796 and tr_G1LX53_G1LX53_AILME_9646 are exactly identical! WARNING: Sequences tr_F6W4W9_F6W4W9_HORSE_9796 and tr_A0A2U4AGJ9_A0A2U4AGJ9_TURTR_9739 are exactly identical! WARNING: Sequences tr_F6W4W9_F6W4W9_HORSE_9796 and tr_A0A2Y9PPE1_A0A2Y9PPE1_DELLE_9749 are exactly identical! WARNING: Sequences tr_F6W4W9_F6W4W9_HORSE_9796 and tr_A0A2Y9SX60_A0A2Y9SX60_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F6W4W9_F6W4W9_HORSE_9796 and tr_A0A384C513_A0A384C513_URSMA_29073 are exactly identical! WARNING: Sequences sp_A0A0A6YYL3_POTEB_HUMAN_9606 and sp_H3BUK9_POTB2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q8N8A2_ANR44_HUMAN_9606 and tr_A0A0D9RGJ7_A0A0D9RGJ7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_Q2UGY0_Q2UGY0_ASPOR_510516 and tr_A0A1S9DZ77_A0A1S9DZ77_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_Q2UN28_Q2UN28_ASPOR_510516 and tr_A0A1S9D6L7_A0A1S9D6L7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A1D5RJR8_A0A1D5RJR8_MACMU_9544 and tr_G7PSM8_G7PSM8_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RJR8_A0A1D5RJR8_MACMU_9544 and tr_A0A2K6E5N0_A0A2K6E5N0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A067H6A7_A0A067H6A7_CITSI_2711 and tr_V4VHF8_V4VHF8_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A096MVX0_A0A096MVX0_PAPAN_9555 and tr_A0A2K5KKK9_A0A2K5KKK9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151NR06_A0A151NR06_ALLMI_8496 and tr_A0A3Q0HN34_A0A3Q0HN34_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091UVR5_A0A091UVR5_NIPNI_128390 and tr_A0A0A0AS26_A0A0A0AS26_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZG8_A0A2D0SZG8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZG9_A0A2D0SZG9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZH1_A0A2D0SZH1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZW2_A0A2D0SZW2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZW7_A0A2D0SZW7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0T0E7_A0A2D0T0E7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0T0F3_A0A2D0T0F3_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 34 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/Q9BXX3/4_raxmlng_ancestral/Q9BXX3.raxml.reduced.phy Alignment comprises 1 partitions and 1397 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1397 Gaps: 70.43 % Invariant sites: 3.87 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXX3/4_raxmlng_ancestral/Q9BXX3.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/Q9BXX3/3_mltree/Q9BXX3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 350 / 28000 [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: -420822.880037 [00:00:00 -420822.880037] Initial branch length optimization [00:00:03 -399180.356534] Model parameter optimization (eps = 0.100000) [00:01:21] Tree #1, final logLikelihood: -397021.511457 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.049572,0.400975) (0.041137,0.359575) (0.413571,0.780370) (0.495720,1.296282) 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/Q9BXX3/4_raxmlng_ancestral/Q9BXX3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXX3/4_raxmlng_ancestral/Q9BXX3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXX3/4_raxmlng_ancestral/Q9BXX3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BXX3/4_raxmlng_ancestral/Q9BXX3.raxml.log Analysis started: 12-Jul-2021 17:52:59 / finished: 12-Jul-2021 17:54:34 Elapsed time: 94.248 seconds Consumed energy: 5.370 Wh