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 02-Jun-2021 18:22:23 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q08830/2_msa/Q08830_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q08830/3_mltree/Q08830.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q08830/4_raxmlng_ancestral/Q08830 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647343 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/Q08830/2_msa/Q08830_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 312 sites WARNING: Sequences tr_F1NE57_F1NE57_CHICK_9031 and tr_A0A0A0B050_A0A0A0B050_CHAVO_50402 are exactly identical! WARNING: Sequences sp_Q9R045_ANGL2_MOUSE_10090 and tr_G3V862_G3V862_RAT_10116 are exactly identical! WARNING: Sequences tr_G1S061_G1S061_NOMLE_61853 and tr_A0A2J8UC26_A0A2J8UC26_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S061_G1S061_NOMLE_61853 and tr_H2Q0P0_H2Q0P0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S061_G1S061_NOMLE_61853 and tr_A0A2R9A861_A0A2R9A861_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and sp_Q9UKU9_ANGL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_F7GXP6_F7GXP6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_U3D4B8_U3D4B8_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_G8F2W1_G8F2W1_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A096P212_A0A096P212_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A0D9RMK9_A0A0D9RMK9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A2K5KRS0_A0A2K5KRS0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A2K6BM30_A0A2K6BM30_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A2K5Z7E9_A0A2K5Z7E9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3T2M5_A0A2I3T2M5_PANTR_9598 and tr_A0A2R9C4Y3_A0A2R9C4Y3_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BRA2_K7BRA2_PANTR_9598 and tr_A0A2R8ZSV1_A0A2R8ZSV1_PANPA_9597 are exactly identical! WARNING: Sequences sp_O43827_ANGL7_HUMAN_9606 and tr_A0A2R9AL00_A0A2R9AL00_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5R9K8_A0A1D5R9K8_MACMU_9544 and tr_G7PTU5_G7PTU5_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R9K8_A0A1D5R9K8_MACMU_9544 and tr_A0A2K5YQP6_A0A2K5YQP6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6UZ20_F6UZ20_MACMU_9544 and tr_G7P6F9_G7P6F9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6UZ20_F6UZ20_MACMU_9544 and tr_A0A2K6D4Y0_A0A2K6D4Y0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DFG3_F7DFG3_MACMU_9544 and tr_G7PRB6_G7PRB6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DFG3_F7DFG3_MACMU_9544 and tr_A0A2K6DIS5_A0A2K6DIS5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HQR6_F7HQR6_MACMU_9544 and tr_A0A096MX05_A0A096MX05_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HQR6_F7HQR6_MACMU_9544 and tr_A0A2K6DZQ6_A0A2K6DZQ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HQR6_F7HQR6_MACMU_9544 and tr_A0A2K6AAY2_A0A2K6AAY2_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9EU04_H9EU04_MACMU_9544 and tr_A0A096MLA3_A0A096MLA3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9EU04_H9EU04_MACMU_9544 and tr_A0A0D9RI18_A0A0D9RI18_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H9EU04_H9EU04_MACMU_9544 and tr_A0A2K5NMC3_A0A2K5NMC3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1ME27_G1ME27_AILME_9646 and tr_M3WA23_M3WA23_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1ME27_G1ME27_AILME_9646 and tr_A0A2U3Y0K3_A0A2U3Y0K3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1ME27_G1ME27_AILME_9646 and tr_A0A2Y9J9L8_A0A2Y9J9L8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1ME27_G1ME27_AILME_9646 and tr_A0A384CQ75_A0A384CQ75_URSMA_29073 are exactly identical! WARNING: Sequences tr_B2Z4B0_B2Z4B0_BOVIN_9913 and tr_A0A2U4CH52_A0A2U4CH52_TURTR_9739 are exactly identical! WARNING: Sequences tr_B2Z4B0_B2Z4B0_BOVIN_9913 and tr_A0A2Y9F761_A0A2Y9F761_PHYCD_9755 are exactly identical! WARNING: Sequences tr_B2Z4B0_B2Z4B0_BOVIN_9913 and tr_A0A384B607_A0A384B607_BALAS_310752 are exactly identical! WARNING: Sequences tr_B2Z4B2_B2Z4B2_BOVIN_9913 and sp_Q24K15_ANGP4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_U3JHQ6_U3JHQ6_FICAL_59894 and tr_A0A091FAC4_A0A091FAC4_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A096P0F6_A0A096P0F6_PAPAN_9555 and tr_A0A2K5LFN1_A0A2K5LFN1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P0F6_A0A096P0F6_PAPAN_9555 and tr_A0A2K6AEG8_A0A2K6AEG8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091IKF7_A0A091IKF7_EGRGA_188379 and tr_A0A091W1Z5_A0A091W1Z5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IKF7_A0A091IKF7_EGRGA_188379 and tr_A0A087QVH7_A0A087QVH7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IKF7_A0A091IKF7_EGRGA_188379 and tr_A0A0A0B078_A0A0A0B078_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091IN85_A0A091IN85_EGRGA_188379 and tr_A0A091VTS8_A0A091VTS8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A2I0LXU7_A0A2I0LXU7_COLLI_8932 and tr_A0A1V4JT28_A0A1V4JT28_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M416_A0A2I0M416_COLLI_8932 and tr_A0A1V4J6J7_A0A1V4J6J7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MC32_A0A2I0MC32_COLLI_8932 and tr_A0A093GN56_A0A093GN56_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A226N2D7_A0A226N2D7_CALSU_9009 and tr_A0A226NXC5_A0A226NXC5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NA62_A0A226NA62_CALSU_9009 and tr_A0A226PC07_A0A226PC07_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NHQ9_A0A226NHQ9_CALSU_9009 and tr_A0A226P3K2_A0A226P3K2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NNT6_A0A226NNT6_CALSU_9009 and tr_A0A226P2C0_A0A226P2C0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0Q894_A0A2D0Q894_ICTPU_7998 and tr_A0A2D0Q9D0_A0A2D0Q9D0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V7E1_A0A2U3V7E1_TURTR_9739 and tr_A0A2Y9F952_A0A2Y9F952_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 53 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/Q08830/4_raxmlng_ancestral/Q08830.raxml.reduced.phy Alignment comprises 1 partitions and 312 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 312 Gaps: 16.13 % Invariant sites: 1.92 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q08830/4_raxmlng_ancestral/Q08830.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/Q08830/3_mltree/Q08830.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 78 / 6240 [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: -128867.959295 [00:00:00 -128867.959295] Initial branch length optimization [00:00:00 -125355.308043] Model parameter optimization (eps = 0.100000) [00:00:14] Tree #1, final logLikelihood: -125312.228724 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.097182,0.094777) (0.173023,0.329930) (0.282981,0.692037) (0.446814,1.651403) 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/Q08830/4_raxmlng_ancestral/Q08830.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q08830/4_raxmlng_ancestral/Q08830.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q08830/4_raxmlng_ancestral/Q08830.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q08830/4_raxmlng_ancestral/Q08830.raxml.log Analysis started: 02-Jun-2021 18:22:23 / finished: 02-Jun-2021 18:22:40 Elapsed time: 17.179 seconds Consumed energy: 1.020 Wh