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 04-Jun-2021 13:57:59 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P47895/2_msa/P47895_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P47895/3_mltree/P47895.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P47895/4_raxmlng_ancestral/P47895 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804279 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_020621/phylogeny-snakemake/results/P47895/2_msa/P47895_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 512 sites WARNING: Sequences sp_O93344_AL1A2_CHICK_9031 and tr_A0A226PKF6_A0A226PKF6_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3XZ73_M3XZ73_MUSPF_9669 and tr_A0A2Y9K310_A0A2Y9K310_ENHLU_391180 are exactly identical! WARNING: Sequences tr_J3K370_J3K370_COCIM_246410 and tr_A0A0J6Y4E5_A0A0J6Y4E5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2VU09_B2VU09_PYRTR_426418 and tr_A0A2W1DHL5_A0A2W1DHL5_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8N8T4_B8N8T4_ASPFN_332952 and tr_Q2UHF6_Q2UHF6_ASPOR_510516 are exactly identical! WARNING: Sequences tr_F1PGT3_F1PGT3_CANLF_9615 and tr_H2Q9I2_H2Q9I2_PANTR_9598 are exactly identical! WARNING: Sequences tr_F1PGT3_F1PGT3_CANLF_9615 and tr_F7CVL4_F7CVL4_HORSE_9796 are exactly identical! WARNING: Sequences tr_F1PGT3_F1PGT3_CANLF_9615 and tr_A0A2R9B140_A0A2R9B140_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3S2X8_A0A2I3S2X8_PANTR_9598 and sp_P00352_AL1A1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3S2X8_A0A2I3S2X8_PANTR_9598 and tr_A0A2R9A203_A0A2R9A203_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QA58_H2QA58_PANTR_9598 and tr_A0A2R9CDK5_A0A2R9CDK5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QXA8_H2QXA8_PANTR_9598 and tr_A0A2R8ZAD4_A0A2R8ZAD4_PANPA_9597 are exactly identical! WARNING: Sequences sp_P05091_ALDH2_HUMAN_9606 and tr_A0A2R8ZCP2_A0A2R8ZCP2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0HNX1_A0A0E0HNX1_ORYNI_4536 and tr_A2YBK1_A2YBK1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HNX1_A0A0E0HNX1_ORYNI_4536 and tr_A0A0E0PW89_A0A0E0PW89_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HNX1_A0A0E0HNX1_ORYNI_4536 and tr_Q9FRX7_Q9FRX7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F6USB4_F6USB4_MACMU_9544 and tr_G7PIP6_G7PIP6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YY71_F6YY71_MACMU_9544 and tr_Q4R5G3_Q4R5G3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YY71_F6YY71_MACMU_9544 and tr_A0A2K6DYN5_A0A2K6DYN5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H3Z0_F7H3Z0_MACMU_9544 and tr_A0A2K6AC29_A0A2K6AC29_MANLE_9568 are exactly identical! WARNING: Sequences tr_I2CVL1_I2CVL1_MACMU_9544 and tr_A0A0D9RHQ6_A0A0D9RHQ6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F9XK58_F9XK58_ZYMTI_336722 and tr_A0A0F4GX37_A0A0F4GX37_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_A8Y3G4_A8Y3G4_CAEBR_6238 and tr_A0A2G5UL98_A0A2G5UL98_9PELO_1611254 are exactly identical! WARNING: Sequences tr_U3KCL4_U3KCL4_FICAL_59894 and tr_A0A218UN47_A0A218UN47_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A096P1S3_A0A096P1S3_PAPAN_9555 and tr_A0A2K5KYV1_A0A2K5KYV1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P1S3_A0A096P1S3_PAPAN_9555 and tr_A0A2K5ZM37_A0A2K5ZM37_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MYH5_A0A2I3MYH5_PAPAN_9555 and tr_A0A2K5P1R7_A0A2K5P1R7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MYH5_A0A2I3MYH5_PAPAN_9555 and tr_A0A2K6CMN2_A0A2K6CMN2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9S3S0_A0A0D9S3S0_CHLSB_60711 and tr_A0A2K5N4C2_A0A2K5N4C2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0F9XDK7_A0A0F9XDK7_TRIHA_5544 and tr_A0A2T4A015_A0A2T4A015_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A091JHV5_A0A091JHV5_EGRGA_188379 and tr_A0A093QB80_A0A093QB80_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091JHV5_A0A091JHV5_EGRGA_188379 and tr_A0A087R468_A0A087R468_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JHV5_A0A091JHV5_EGRGA_188379 and tr_A0A091G7A0_A0A091G7A0_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0G4PQ94_A0A0G4PQ94_PENCA_1429867 and tr_A0A101M936_A0A101M936_9EURO_48697 are exactly identical! WARNING: Sequences tr_A0A2I0M6Q2_A0A2I0M6Q2_COLLI_8932 and tr_A0A1V4JDV7_A0A1V4JDV7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CI63_A0A0V1CI63_TRIBR_45882 and tr_A0A0V1PAT5_A0A0V1PAT5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CI63_A0A0V1CI63_TRIBR_45882 and tr_A0A0V0TGY7_A0A0V0TGY7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0W756_A0A0V0W756_9BILA_92179 and tr_A0A0V0VK60_A0A0V0VK60_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A1S3Z2K5_A0A1S3Z2K5_TOBAC_4097 and tr_A0A1U7V091_A0A1U7V091_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1U7QDB4_A0A1U7QDB4_MESAU_10036 and sp_P86886_AL1A1_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A1V8UM63_A0A1V8UM63_9PEZI_1974281 and tr_A0A1V8SM42_A0A1V8SM42_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A226NNL0_A0A226NNL0_CALSU_9009 and tr_A0A226PE42_A0A226PE42_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2G5H9I5_A0A2G5H9I5_CERBT_122368 and tr_A0A2S6BS70_A0A2S6BS70_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2U4BAL8_A0A2U4BAL8_TURTR_9739 and tr_A0A2Y9NIU5_A0A2Y9NIU5_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 44 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P47895/4_raxmlng_ancestral/P47895.raxml.reduced.phy Alignment comprises 1 partitions and 512 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 512 Gaps: 4.03 % Invariant sites: 1.37 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P47895/4_raxmlng_ancestral/P47895.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_020621/phylogeny-snakemake/results/P47895/3_mltree/P47895.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 128 / 10240 [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: -170545.069006 [00:00:00 -170545.069006] Initial branch length optimization [00:00:01 -168853.827410] Model parameter optimization (eps = 0.100000) [00:00:27] Tree #1, final logLikelihood: -168275.610325 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.237594,0.367677) (0.320088,0.559392) (0.253617,1.078045) (0.188700,2.438666) 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_020621/phylogeny-snakemake/results/P47895/4_raxmlng_ancestral/P47895.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P47895/4_raxmlng_ancestral/P47895.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P47895/4_raxmlng_ancestral/P47895.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P47895/4_raxmlng_ancestral/P47895.raxml.log Analysis started: 04-Jun-2021 13:57:59 / finished: 04-Jun-2021 13:58:31 Elapsed time: 31.729 seconds