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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 20-Jul-2021 16:33:47 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/2_msa/P19532_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/3_mltree/P19532.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/4_raxmlng_ancestral/P19532 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626788027 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/2_msa/P19532_nogap_msa.fasta [00:00:00] Loaded alignment with 903 taxa and 575 sites WARNING: Sequences sp_Q64705_USF2_MOUSE_10090 and sp_Q63665_USF2_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YQ82_M3YQ82_MUSPF_9669 and tr_A0A2Y9JDZ6_A0A2Y9JDZ6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1QYE3_G1QYE3_NOMLE_61853 and tr_F7FXN6_F7FXN6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QYE3_G1QYE3_NOMLE_61853 and tr_A0A096NI31_A0A096NI31_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QYE3_G1QYE3_NOMLE_61853 and tr_A0A2K5LZY5_A0A2K5LZY5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QYE3_G1QYE3_NOMLE_61853 and tr_A0A2K6CP29_A0A2K6CP29_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2YS93_A0A2I2YS93_GORGO_9595 and sp_P19532_TFE3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YXN7_A0A2I2YXN7_GORGO_9595 and sp_O75030_MITF_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YXN7_A0A2I2YXN7_GORGO_9595 and tr_G7NZ88_G7NZ88_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2YXN7_A0A2I2YXN7_GORGO_9595 and tr_A0A2K5ZRN7_A0A2K5ZRN7_MANLE_9568 are exactly identical! WARNING: Sequences tr_B8P4X4_B8P4X4_POSPM_561896 and tr_A0A1X6MPE3_A0A1X6MPE3_9APHY_670580 are exactly identical! WARNING: Sequences sp_Q15853_USF2_HUMAN_9606 and tr_I0FUV2_I0FUV2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A1D5QUV2_A0A1D5QUV2_MACMU_9544 and tr_G7P2I1_G7P2I1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QUV2_A0A1D5QUV2_MACMU_9544 and tr_A0A2K6ALQ3_A0A2K6ALQ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QWQ4_A0A1D5QWQ4_MACMU_9544 and tr_A0A096P323_A0A096P323_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6UXQ5_F6UXQ5_MACMU_9544 and tr_A0A2K5MJT8_A0A2K5MJT8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_G7Q2P5_G7Q2P5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A0D9RKQ6_A0A0D9RKQ6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A2K5LC64_A0A2K5LC64_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A2K6CFN5_A0A2K6CFN5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7E2P9_F7E2P9_MACMU_9544 and tr_A0A2K5ZD31_A0A2K5ZD31_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FA74_F7FA74_CALJA_9483 and tr_A0A2I3M2E5_A0A2I3M2E5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FA74_F7FA74_CALJA_9483 and tr_A0A0D9RGQ2_A0A0D9RGQ2_CHLSB_60711 are exactly identical! WARNING: Sequences sp_A4IFU7_TFEC_BOVIN_9913 and tr_F1ML66_F1ML66_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A337SGF3_A0A337SGF3_FELCA_9685 and tr_A0A2U3X4F1_A0A2U3X4F1_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A337SGF3_A0A337SGF3_FELCA_9685 and tr_A0A2Y9L605_A0A2Y9L605_ENHLU_391180 are exactly identical! WARNING: Sequences tr_V2XHX0_V2XHX0_MONRO_1381753 and tr_A0A0W0FMJ9_A0A0W0FMJ9_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A0A1MH28_A0A0A1MH28_9FUNG_58291 and tr_A0A367KBH5_A0A367KBH5_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091KDI0_A0A091KDI0_EGRGA_188379 and tr_A0A087RBZ2_A0A087RBZ2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091KDI0_A0A091KDI0_EGRGA_188379 and tr_A0A093FWR9_A0A093FWR9_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A165D7J5_A0A165D7J5_EXIGL_1314781 and tr_A0A165IP52_A0A165IP52_EXIGL_1314781 are exactly identical! WARNING: Sequences tr_A0A2H3CJD7_A0A2H3CJD7_9AGAR_1076256 and tr_A0A284QU00_A0A284QU00_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2D0PPZ9_A0A2D0PPZ9_ICTPU_7998 and tr_A0A2D0PSM2_A0A2D0PSM2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYF8_A0A2D0QYF8_ICTPU_7998 and tr_A0A2D0QYQ1_A0A2D0QYQ1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYG2_A0A2D0QYG2_ICTPU_7998 and tr_A0A2D0R090_A0A2D0R090_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V0J3_A0A2U3V0J3_TURTR_9739 and tr_A0A2U3V0J9_A0A2U3V0J9_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4CCY7_A0A2U4CCY7_TURTR_9739 and tr_A0A2U4CCZ3_A0A2U4CCZ3_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2Y9NU69_A0A2Y9NU69_DELLE_9749 and tr_A0A2Y9FDH8_A0A2Y9FDH8_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 38 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/4_raxmlng_ancestral/P19532.raxml.reduced.phy Alignment comprises 1 partitions and 575 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 575 Gaps: 46.44 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/4_raxmlng_ancestral/P19532.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/3_mltree/P19532.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 144 / 11520 [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: -168164.439934 [00:00:00 -168164.439934] Initial branch length optimization [00:00:01 -166754.673790] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -166050.122761 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.067831,0.307431) (0.077632,0.767662) (0.298854,0.693160) (0.555683,1.282023) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/4_raxmlng_ancestral/P19532.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/4_raxmlng_ancestral/P19532.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/4_raxmlng_ancestral/P19532.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P19532/4_raxmlng_ancestral/P19532.raxml.log Analysis started: 20-Jul-2021 16:33:47 / finished: 20-Jul-2021 16:34:33 Elapsed time: 46.361 seconds