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 16:32:05 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MCN3/2_msa/B5MCN3_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MCN3/3_mltree/B5MCN3.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MCN3/4_raxmlng_ancestral/B5MCN3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626787925 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/B5MCN3/2_msa/B5MCN3_nogap_msa.fasta [00:00:00] Loaded alignment with 730 taxa and 397 sites WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_G1MXX5_G1MXX5_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_H0ZBN5_H0ZBN5_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_U3JDN1_U3JDN1_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_U3IE46_U3IE46_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_A0A091F6Y0_A0A091F6Y0_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_A0A091J5R3_A0A091J5R3_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_A0A093SNR5_A0A093SNR5_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_A0A091UQH0_A0A091UQH0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_A0A091FMD7_A0A091FMD7_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_A0A2I0M7M2_A0A2I0M7M2_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_A0A091IDJ2_A0A091IDJ2_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_A0A1V4KW31_A0A1V4KW31_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5P5E8_A0A1D5P5E8_CHICK_9031 and tr_A0A218UJU7_A0A218UJU7_9PASE_299123 are exactly identical! WARNING: Sequences tr_H2NUV0_H2NUV0_PONAB_9601 and tr_H2RCN1_H2RCN1_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NUV0_H2NUV0_PONAB_9601 and sp_Q92503_S14L1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NUV0_H2NUV0_PONAB_9601 and tr_F6U5Q0_F6U5Q0_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2NUV0_H2NUV0_PONAB_9601 and tr_G8F5S7_G8F5S7_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2NUV0_H2NUV0_PONAB_9601 and tr_A0A096NT53_A0A096NT53_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2NUV0_H2NUV0_PONAB_9601 and tr_A0A0D9QYL4_A0A0D9QYL4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NUV0_H2NUV0_PONAB_9601 and tr_A0A2K5NZZ1_A0A2K5NZZ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NUV0_H2NUV0_PONAB_9601 and tr_A0A2K5ZBV7_A0A2K5ZBV7_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2NUV0_H2NUV0_PONAB_9601 and tr_A0A2R9BBZ1_A0A2R9BBZ1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QAJ0_H2QAJ0_PANTR_9598 and tr_A0A2R9BC04_A0A2R9BC04_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5P8J1_W5P8J1_SHEEP_9940 and tr_A7MBE2_A7MBE2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F7HAA2_F7HAA2_MACMU_9544 and tr_G7PF68_G7PF68_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HAA2_F7HAA2_MACMU_9544 and tr_A0A2K5NBZ8_A0A2K5NBZ8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HAA2_F7HAA2_MACMU_9544 and tr_A0A2K6BZB5_A0A2K6BZB5_MACNE_9545 are exactly identical! WARNING: Sequences tr_B3S552_B3S552_TRIAD_10228 and tr_A0A369SHW7_A0A369SHW7_9METZ_287889 are exactly identical! WARNING: Sequences tr_G7PF71_G7PF71_MACFA_9541 and tr_A0A2K5ZQS4_A0A2K5ZQS4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PF71_G7PF71_MACFA_9541 and tr_A0A2R9CMK1_A0A2R9CMK1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0F8XBU3_A0A0F8XBU3_9EURO_308745 and tr_A0A2T5LMA2_A0A2T5LMA2_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A151N3C5_A0A151N3C5_ALLMI_8496 and tr_A0A3Q0G1C8_A0A3Q0G1C8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151N6Q0_A0A151N6Q0_ALLMI_8496 and tr_A0A1U7RCL5_A0A1U7RCL5_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0V0WUH9_A0A0V0WUH9_9BILA_92179 and tr_A0A0V1LFT6_A0A0V1LFT6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WUH9_A0A0V0WUH9_9BILA_92179 and tr_A0A0V0ZXY4_A0A0V0ZXY4_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A1S3RAC0_A0A1S3RAC0_SALSA_8030 and tr_A0A1S3S3Q8_A0A1S3S3Q8_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1I7TEG9_A0A1I7TEG9_9PELO_1561998 and tr_A0A1I7TEH0_A0A1I7TEH0_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A226NED7_A0A226NED7_CALSU_9009 and tr_A0A226PAA1_A0A226PAA1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4BMC2_A0A2U4BMC2_TURTR_9739 and tr_A0A2Y9PQR5_A0A2Y9PQR5_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 39 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/B5MCN3/4_raxmlng_ancestral/B5MCN3.raxml.reduced.phy Alignment comprises 1 partitions and 397 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 397 Gaps: 15.40 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MCN3/4_raxmlng_ancestral/B5MCN3.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/B5MCN3/3_mltree/B5MCN3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 100 / 8000 [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: -154441.358462 [00:00:00 -154441.358462] Initial branch length optimization [00:00:00 -152809.464582] Model parameter optimization (eps = 0.100000) [00:00:26] Tree #1, final logLikelihood: -152117.292919 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.115545,0.670625) (0.161212,0.677139) (0.425473,0.834916) (0.297769,1.538489) 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/B5MCN3/4_raxmlng_ancestral/B5MCN3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MCN3/4_raxmlng_ancestral/B5MCN3.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MCN3/4_raxmlng_ancestral/B5MCN3.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B5MCN3/4_raxmlng_ancestral/B5MCN3.raxml.log Analysis started: 20-Jul-2021 16:32:05 / finished: 20-Jul-2021 16:32:34 Elapsed time: 29.181 seconds