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 14-Jul-2021 13:54:12 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y575/2_msa/Q9Y575_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y575/3_mltree/Q9Y575.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y575/4_raxmlng_ancestral/Q9Y575 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626260052 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/Q9Y575/2_msa/Q9Y575_nogap_msa.fasta [00:00:00] Loaded alignment with 979 taxa and 518 sites WARNING: Sequences tr_B4Q8M0_B4Q8M0_DROSI_7240 and tr_Q9VQI1_Q9VQI1_DROME_7227 are exactly identical! WARNING: Sequences tr_F1NLN5_F1NLN5_CHICK_9031 and tr_A0A226PZ47_A0A226PZ47_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3Z111_M3Z111_MUSPF_9669 and tr_I3LD98_I3LD98_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z111_M3Z111_MUSPF_9669 and tr_A0A2Y9KE62_A0A2Y9KE62_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z111_M3Z111_MUSPF_9669 and tr_A0A384BYR1_A0A384BYR1_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3G1Z7_A0A2I3G1Z7_NOMLE_61853 and tr_G3SG36_G3SG36_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3G1Z7_A0A2I3G1Z7_NOMLE_61853 and tr_H2PGS0_H2PGS0_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3G1Z7_A0A2I3G1Z7_NOMLE_61853 and tr_K7DU15_K7DU15_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3G1Z7_A0A2I3G1Z7_NOMLE_61853 and sp_Q8IWZ3_ANKH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B6QHD1_B6QHD1_TALMQ_441960 and tr_A0A093VHE0_A0A093VHE0_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2I2Z799_A0A2I2Z799_GORGO_9595 and sp_Q9Y575_ASB3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B5DJU8_B5DJU8_DROPS_46245 and tr_B4GSC2_B4GSC2_DROPE_7234 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_I3LZI0_I3LZI0_ICTTR_43179 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2U4AGJ9_A0A2U4AGJ9_TURTR_9739 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2Y9PPE1_A0A2Y9PPE1_DELLE_9749 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2Y9SX60_A0A2Y9SX60_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A384B3D1_A0A384B3D1_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2I3SXH5_A0A2I3SXH5_PANTR_9598 and tr_A0A2R9BJ86_A0A2R9BJ86_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R3M2_H2R3M2_PANTR_9598 and sp_P16157_ANK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R3M2_H2R3M2_PANTR_9598 and tr_F6Y8R2_F6Y8R2_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2R3M2_H2R3M2_PANTR_9598 and tr_A0A0D9RRD4_A0A0D9RRD4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2R3M2_H2R3M2_PANTR_9598 and tr_A0A2R9AEU3_A0A2R9AEU3_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5Q672_W5Q672_SHEEP_9940 and tr_E1B7G6_E1B7G6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5Q8W7_W5Q8W7_SHEEP_9940 and tr_E1B719_E1B719_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A087ZS21_A0A087ZS21_APIME_7460 and tr_A0A2A3E9M4_A0A2A3E9M4_APICC_94128 are exactly identical! WARNING: Sequences tr_Q2UGY0_Q2UGY0_ASPOR_510516 and tr_A0A1S9DZ77_A0A1S9DZ77_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_F6ZH85_F6ZH85_MACMU_9544 and tr_G7P8G5_G7P8G5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6ZH85_F6ZH85_MACMU_9544 and tr_A0A2I3N6E9_A0A2I3N6E9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6ZH85_F6ZH85_MACMU_9544 and tr_A0A0D9RK88_A0A0D9RK88_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6ZH85_F6ZH85_MACMU_9544 and tr_A0A2K5Y5C2_A0A2K5Y5C2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7BJ78_F7BJ78_MACMU_9544 and tr_A0A2K6DUH2_A0A2K6DUH2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0YUA6_H0YUA6_TAEGU_59729 and tr_A0A218UPI7_A0A218UPI7_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0YUX9_H0YUX9_TAEGU_59729 and tr_A0A091EUN4_A0A091EUN4_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YUX9_H0YUX9_TAEGU_59729 and tr_A0A218UXQ1_A0A218UXQ1_9PASE_299123 are exactly identical! WARNING: Sequences tr_G1LX53_G1LX53_AILME_9646 and tr_A0A384C513_A0A384C513_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1N2S1_F1N2S1_BOVIN_9913 and sp_Q3SX45_ASB2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A151NV64_A0A151NV64_ALLMI_8496 and tr_A0A3Q0GHR3_A0A3Q0GHR3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091UIT4_A0A091UIT4_NIPNI_128390 and tr_A0A087R3L6_A0A087R3L6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A087QKS1_A0A087QKS1_APTFO_9233 and tr_A0A2I0MGU1_A0A2I0MGU1_COLLI_8932 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: Sequences tr_A0A2K5MAP3_A0A2K5MAP3_CERAT_9531 and tr_A0A2K6DC65_A0A2K6DC65_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U3ZD56_A0A2U3ZD56_ODORO_9708 and tr_A0A2U3XJ53_A0A2U3XJ53_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 48 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/Q9Y575/4_raxmlng_ancestral/Q9Y575.raxml.reduced.phy Alignment comprises 1 partitions and 518 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 518 Gaps: 30.05 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y575/4_raxmlng_ancestral/Q9Y575.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/Q9Y575/3_mltree/Q9Y575.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 130 / 10400 [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: -427112.722150 [00:00:00 -427112.722150] Initial branch length optimization [00:00:02 -345090.164443] Model parameter optimization (eps = 0.100000) [00:01:04] Tree #1, final logLikelihood: -343416.996732 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.131115,0.337704) (0.130597,0.383634) (0.409837,0.996051) (0.328451,1.514386) 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/Q9Y575/4_raxmlng_ancestral/Q9Y575.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y575/4_raxmlng_ancestral/Q9Y575.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y575/4_raxmlng_ancestral/Q9Y575.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y575/4_raxmlng_ancestral/Q9Y575.raxml.log Analysis started: 14-Jul-2021 13:54:12 / finished: 14-Jul-2021 13:55:21 Elapsed time: 68.792 seconds