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 18:13:56 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92766/2_msa/Q92766_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92766/3_mltree/Q92766.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92766/4_raxmlng_ancestral/Q92766 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102836 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/Q92766/2_msa/Q92766_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1687 sites WARNING: Sequences tr_A0A2I2Y2H9_A0A2I2Y2H9_GORGO_9595 and tr_A0A2J8S1I3_A0A2J8S1I3_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Y2H9_A0A2I2Y2H9_GORGO_9595 and sp_Q9BUY5_ZN426_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_H2NR83_H2NR83_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_H2QBB9_H2QBB9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_H0X5R9_H0X5R9_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and sp_P49711_CTCF_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_G7NQ61_G7NQ61_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_G5E6X2_G5E6X2_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_G8F4K8_G8F4K8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_Q08DH9_Q08DH9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A096NZP9_A0A096NZP9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A0D9QV86_A0A0D9QV86_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A3Q0EDC7_A0A3Q0EDC7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A2K5NS86_A0A2K5NS86_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A2K6CQN4_A0A2K6CQN4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A2K6A1T9_A0A2K6A1T9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A2R9CRW2_A0A2R9CRW2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A2U4BDE5_A0A2U4BDE5_TURTR_9739 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A2Y9NYV3_A0A2Y9NYV3_DELLE_9749 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A2Y9SXZ5_A0A2Y9SXZ5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A384BEM0_A0A384BEM0_BALAS_310752 are exactly identical! WARNING: Sequences tr_G3RFD0_G3RFD0_GORGO_9595 and tr_H2QFF8_H2QFF8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RFD0_G3RFD0_GORGO_9595 and sp_Q8TA94_ZN563_HUMAN_9606 are exactly identical! WARNING: Sequences tr_E2RJR9_E2RJR9_CANLF_9615 and tr_I3MZ84_I3MZ84_ICTTR_43179 are exactly identical! WARNING: Sequences tr_E2RJR9_E2RJR9_CANLF_9615 and tr_G1MGF9_G1MGF9_AILME_9646 are exactly identical! WARNING: Sequences tr_E2RJR9_E2RJR9_CANLF_9615 and tr_A0A2Y9K1L7_A0A2Y9K1L7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_E2RJR9_E2RJR9_CANLF_9615 and tr_A0A384D1P4_A0A384D1P4_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3STQ8_A0A2I3STQ8_PANTR_9598 and tr_A0A2R8ZUA2_A0A2R8ZUA2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QKN0_H2QKN0_PANTR_9598 and tr_A0A2R9AR17_A0A2R9AR17_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NHM0_A0A158NHM0_ATTCE_12957 and tr_A0A151I603_A0A151I603_9HYME_520822 are exactly identical! WARNING: Sequences sp_A8MT65_ZN891_HUMAN_9606 and tr_A0A2R8Z7T5_A0A2R8Z7T5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QXZ3_A0A1D5QXZ3_MACMU_9544 and tr_G7PZ52_G7PZ52_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QXZ3_A0A1D5QXZ3_MACMU_9544 and tr_A0A2K6D4T1_A0A2K6D4T1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WQ38_F6WQ38_MACMU_9544 and tr_G7PRN1_G7PRN1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WQ38_F6WQ38_MACMU_9544 and tr_A0A2K6DYU0_A0A2K6DYU0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7A732_F7A732_MACMU_9544 and tr_A0A2K6E112_A0A2K6E112_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7A7M4_F7A7M4_MACMU_9544 and tr_G7PZ49_G7PZ49_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7A7M4_F7A7M4_MACMU_9544 and tr_A0A2K6DUY9_A0A2K6DUY9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7A7M4_F7A7M4_MACMU_9544 and tr_A0A2K5XT92_A0A2K5XT92_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7H8Y3_F7H8Y3_MACMU_9544 and tr_G7PZ51_G7PZ51_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7IC32_F7IC32_CALJA_9483 and tr_I3LDG5_I3LDG5_PIG_9823 are exactly identical! WARNING: Sequences tr_G7PFS9_G7PFS9_MACFA_9541 and tr_A0A2K5Y9Z0_A0A2K5Y9Z0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A044TQV9_A0A044TQV9_ONCVO_6282 and tr_A0A182E4H2_A0A182E4H2_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0A0MU12_A0A0A0MU12_PAPAN_9555 and tr_A0A2K5KTK7_A0A2K5KTK7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0A0MVB6_A0A0A0MVB6_PAPAN_9555 and tr_A0A2K6D383_A0A2K6D383_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151NJM4_A0A151NJM4_ALLMI_8496 and tr_A0A1U7S702_A0A1U7S702_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A2D0RZ52_A0A2D0RZ52_ICTPU_7998 and tr_A0A2D0S023_A0A2D0S023_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LPU1_A0A2K5LPU1_CERAT_9531 and tr_A0A2K6A833_A0A2K6A833_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3V5W8_A0A2U3V5W8_TURTR_9739 and tr_A0A2U4CH49_A0A2U4CH49_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2Y9EGH1_A0A2Y9EGH1_PHYCD_9755 and tr_A0A384B4Y9_A0A384B4Y9_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 50 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/Q92766/4_raxmlng_ancestral/Q92766.raxml.reduced.phy Alignment comprises 1 partitions and 1687 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1687 Gaps: 70.12 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92766/4_raxmlng_ancestral/Q92766.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/Q92766/3_mltree/Q92766.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 422 / 33760 [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: -391178.487107 [00:00:00 -391178.487107] Initial branch length optimization [00:00:03 -383897.344274] Model parameter optimization (eps = 0.100000) [00:02:21] Tree #1, final logLikelihood: -382688.642904 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.056963,0.195447) (0.055869,0.548016) (0.317704,0.645728) (0.569464,1.322470) 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/Q92766/4_raxmlng_ancestral/Q92766.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92766/4_raxmlng_ancestral/Q92766.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92766/4_raxmlng_ancestral/Q92766.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92766/4_raxmlng_ancestral/Q92766.raxml.log Analysis started: 12-Jul-2021 18:13:56 / finished: 12-Jul-2021 18:16:33 Elapsed time: 157.135 seconds Consumed energy: 12.995 Wh