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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 12-Jul-2021 18:26:49 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/2_msa/Q92824_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/3_mltree/Q92824.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/4_raxmlng_ancestral/Q92824 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626103609 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/Q92824/2_msa/Q92824_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 1860 sites WARNING: Sequences tr_B4QWQ8_B4QWQ8_DROSI_7240 and tr_B4ICP4_B4ICP4_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and sp_Q5REC2_NEC2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_H2QJZ8_H2QJZ8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_F7GNE5_F7GNE5_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_G7PH08_G7PH08_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_A0A2I3LHF8_A0A2I3LHF8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_A0A0D9RGX4_A0A0D9RGX4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_A0A2R9C4T7_A0A2R9C4T7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QA34_H2QA34_PANTR_9598 and tr_A0A2R9B4W5_A0A2R9B4W5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A088AB96_A0A088AB96_APIME_7460 and tr_A0A2A3ES43_A0A2A3ES43_APICC_94128 are exactly identical! WARNING: Sequences tr_G7MVY8_G7MVY8_MACMU_9544 and tr_G7P9G7_G7P9G7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MVY8_G7MVY8_MACMU_9544 and tr_A0A2K6CBX3_A0A2K6CBX3_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9FVB9_H9FVB9_MACMU_9544 and tr_A0A2K6B7M1_A0A2K6B7M1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3UKG4_G3UKG4_LOXAF_9785 and tr_A0A2Y9DKR5_A0A2Y9DKR5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A8X8V5_A8X8V5_CAEBR_6238 and tr_A0A2G5TIU1_A0A2G5TIU1_9PELO_1611254 are exactly identical! WARNING: Sequences tr_B3RSJ2_B3RSJ2_TRIAD_10228 and tr_A0A369SHI3_A0A369SHI3_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V1D7D4_A0A0V1D7D4_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V0W964_A0A0V0W964_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V0UUJ0_A0A0V0UUJ0_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V1L1V1_A0A0V1L1V1_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V1NVA9_A0A0V1NVA9_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V0TPY5_A0A0V0TPY5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1CXQ2_A0A0V1CXQ2_TRIBR_45882 and tr_A0A0V0WZ98_A0A0V0WZ98_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CXQ2_A0A0V1CXQ2_TRIBR_45882 and tr_A0A0V0VID3_A0A0V0VID3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CXQ2_A0A0V1CXQ2_TRIBR_45882 and tr_A0A0V1A1P5_A0A0V1A1P5_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CXQ2_A0A0V1CXQ2_TRIBR_45882 and tr_A0A0V0U5L3_A0A0V0U5L3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A226N5B8_A0A226N5B8_CALSU_9009 and tr_A0A226PCB9_A0A226PCB9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RWE6_A0A2D0RWE6_ICTPU_7998 and tr_A0A2D0RX26_A0A2D0RX26_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3WSM1_A0A2U3WSM1_ODORO_9708 and tr_A0A2U3YKQ6_A0A2U3YKQ6_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 29 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/Q92824/4_raxmlng_ancestral/Q92824.raxml.reduced.phy Alignment comprises 1 partitions and 1860 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1860 Gaps: 58.80 % Invariant sites: 1.29 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/4_raxmlng_ancestral/Q92824.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/Q92824/3_mltree/Q92824.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 465 / 37200 [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: -451528.597571 [00:00:00 -451528.597571] Initial branch length optimization [00:00:04 -415752.154901] Model parameter optimization (eps = 0.100000) [00:01:38] Tree #1, final logLikelihood: -414375.406977 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.205183,0.240079) (0.073542,0.348514) (0.302002,0.772649) (0.419273,1.649923) 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/Q92824/4_raxmlng_ancestral/Q92824.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/4_raxmlng_ancestral/Q92824.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/4_raxmlng_ancestral/Q92824.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/4_raxmlng_ancestral/Q92824.raxml.log Analysis started: 12-Jul-2021 18:26:49 / finished: 12-Jul-2021 18:28:44 Elapsed time: 114.451 seconds Consumed energy: 5.634 Wh