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 13:44:59 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00222/2_msa/O00222_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00222/3_mltree/O00222.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00222/4_raxmlng_ancestral/O00222 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803499 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/O00222/2_msa/O00222_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 908 sites WARNING: Sequences tr_E1BUE5_E1BUE5_CHICK_9031 and tr_G1N0U8_G1N0U8_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NWG3_F1NWG3_CHICK_9031 and tr_G3UV46_G3UV46_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q3UVX5_GRM5_MOUSE_10090 and sp_P31424_GRM5_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z2Y6_M3Z2Y6_MUSPF_9669 and tr_A0A2U3XYC5_A0A2U3XYC5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2I3GBH9_A0A2I3GBH9_NOMLE_61853 and tr_H2QTV8_H2QTV8_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GBH9_A0A2I3GBH9_NOMLE_61853 and sp_Q13255_GRM1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GBH9_A0A2I3GBH9_NOMLE_61853 and tr_A0A2R9CQ41_A0A2R9CQ41_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SKH7_G3SKH7_GORGO_9595 and tr_F7IRR1_F7IRR1_CALJA_9483 are exactly identical! WARNING: Sequences tr_C7G3M9_C7G3M9_PANTR_9598 and tr_A0A2R9CHT6_A0A2R9CHT6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q4J0_H2Q4J0_PANTR_9598 and sp_P41594_GRM5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R892_H2R892_PANTR_9598 and tr_A0A2R8ZPS6_A0A2R8ZPS6_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6SR09_F6SR09_MACMU_9544 and tr_A0A096MW30_A0A096MW30_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6SR09_F6SR09_MACMU_9544 and tr_A0A2K5N6Z9_A0A2K5N6Z9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6SR09_F6SR09_MACMU_9544 and tr_A0A2K6CBZ4_A0A2K6CBZ4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VUY3_F6VUY3_MACMU_9544 and tr_A0A2K5M1W1_A0A2K5M1W1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6VUY3_F6VUY3_MACMU_9544 and tr_A0A2K6D5Q4_A0A2K6D5Q4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VUY3_F6VUY3_MACMU_9544 and tr_A0A2K5ZF92_A0A2K5ZF92_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6WXK4_F6WXK4_MACMU_9544 and tr_A0A096NWD6_A0A096NWD6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WXK4_F6WXK4_MACMU_9544 and tr_A0A2K5N5W1_A0A2K5N5W1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WXK4_F6WXK4_MACMU_9544 and tr_A0A2K6AHX7_A0A2K6AHX7_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6YNZ0_F6YNZ0_MACMU_9544 and tr_G7P1W4_G7P1W4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YNZ0_F6YNZ0_MACMU_9544 and tr_A0A096NQX7_A0A096NQX7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6YNZ0_F6YNZ0_MACMU_9544 and tr_A0A2K5MFQ8_A0A2K5MFQ8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H091_F7H091_MACMU_9544 and tr_G7NZX8_G7NZX8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H091_F7H091_MACMU_9544 and tr_A0A2K6AXH9_A0A2K6AXH9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MRR5_G7MRR5_MACMU_9544 and tr_A0A2K5L4B3_A0A2K5L4B3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MRR5_G7MRR5_MACMU_9544 and tr_A0A2K5ZRK7_A0A2K5ZRK7_MANLE_9568 are exactly identical! WARNING: Sequences tr_E3LW39_E3LW39_CAERE_31234 and tr_A0A261CEH5_A0A261CEH5_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A0A337SVS1_A0A337SVS1_FELCA_9685 and tr_A0A2Y9J2R9_A0A2Y9J2R9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_U3JZL0_U3JZL0_FICAL_59894 and tr_A0A218V5W0_A0A218V5W0_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A096NAZ6_A0A096NAZ6_PAPAN_9555 and tr_A0A2K6DGW0_A0A2K6DGW0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NYH1_A0A096NYH1_PAPAN_9555 and tr_A0A2K5MDE4_A0A2K5MDE4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NYH1_A0A096NYH1_PAPAN_9555 and tr_A0A2K5XPW0_A0A2K5XPW0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0K0EYK3_A0A0K0EYK3_STRVS_75913 and tr_A0A0N5BML5_A0A0N5BML5_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A2I0MHA0_A0A2I0MHA0_COLLI_8932 and tr_A0A1V4K090_A0A1V4K090_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CS78_A0A0V1CS78_TRIBR_45882 and tr_A0A0V0VQR5_A0A0V0VQR5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CS78_A0A0V1CS78_TRIBR_45882 and tr_A0A0V0U1E0_A0A0V0U1E0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1MD76_A0A0V1MD76_9BILA_268474 and tr_A0A0V1H5Y0_A0A0V1H5Y0_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A226NL75_A0A226NL75_CALSU_9009 and tr_A0A226P255_A0A226P255_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4B1P1_A0A2U4B1P1_TURTR_9739 and tr_A0A2Y9PM51_A0A2Y9PM51_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 40 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/O00222/4_raxmlng_ancestral/O00222.raxml.reduced.phy Alignment comprises 1 partitions and 908 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 908 Gaps: 12.14 % Invariant sites: 0.33 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00222/4_raxmlng_ancestral/O00222.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/O00222/3_mltree/O00222.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 227 / 18160 [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: -253219.110083 [00:00:00 -253219.110083] Initial branch length optimization [00:00:02 -247632.936524] Model parameter optimization (eps = 0.100000) [00:00:54] Tree #1, final logLikelihood: -247075.636464 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.200468,0.246383) (0.240005,0.349303) (0.359194,0.986962) (0.200333,2.557062) 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/O00222/4_raxmlng_ancestral/O00222.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00222/4_raxmlng_ancestral/O00222.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00222/4_raxmlng_ancestral/O00222.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00222/4_raxmlng_ancestral/O00222.raxml.log Analysis started: 04-Jun-2021 13:44:59 / finished: 04-Jun-2021 13:46:02 Elapsed time: 62.555 seconds