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 17-Jul-2021 08:29:41 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RNN3/2_msa/B2RNN3_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RNN3/3_mltree/B2RNN3.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RNN3/4_raxmlng_ancestral/B2RNN3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626499781 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/B2RNN3/2_msa/B2RNN3_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 333 sites WARNING: Sequences tr_G1QSI7_G1QSI7_NOMLE_61853 and tr_H2QT85_H2QT85_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3IID2_G3IID2_CRIGR_10029 and tr_A0A1U8BXJ7_A0A1U8BXJ7_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QSG2_G3QSG2_GORGO_9595 and tr_H2QRX8_H2QRX8_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PCY3_H2PCY3_PONAB_9601 and tr_A0A0D9RV09_A0A0D9RV09_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3S1X9_A0A2I3S1X9_PANTR_9598 and sp_A6NHN0_OTOL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SKI3_A0A2I3SKI3_PANTR_9598 and tr_A0A2R8Z6A0_A0A2R8Z6A0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8K450_A0A2J8K450_PANTR_9598 and tr_A0A2R9A2B8_A0A2R9A2B8_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6VWB8_F6VWB8_MACMU_9544 and tr_A0A096MVD2_A0A096MVD2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6VWB8_F6VWB8_MACMU_9544 and tr_A0A2K5LUF6_A0A2K5LUF6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6VWB8_F6VWB8_MACMU_9544 and tr_A0A2K6BMA7_A0A2K6BMA7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VWB8_F6VWB8_MACMU_9544 and tr_A0A2K5ZRM9_A0A2K5ZRM9_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6ZZB7_F6ZZB7_MACMU_9544 and tr_A0A2K6DXC5_A0A2K6DXC5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_A0A2K5MIM6_A0A2K5MIM6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_A0A2K6B809_A0A2K6B809_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_A0A2K5YA30_A0A2K5YA30_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FYZ2_F7FYZ2_MACMU_9544 and tr_A0A2K5M5S7_A0A2K5M5S7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FYZ2_F7FYZ2_MACMU_9544 and tr_A0A2K6CSK8_A0A2K6CSK8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FYZ2_F7FYZ2_MACMU_9544 and tr_A0A2K5ZT07_A0A2K5ZT07_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HEL0_F7HEL0_MACMU_9544 and tr_G7NVT9_G7NVT9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HEL0_F7HEL0_MACMU_9544 and tr_A0A2I3NGK8_A0A2I3NGK8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HEL0_F7HEL0_MACMU_9544 and tr_A0A2K6AVT3_A0A2K6AVT3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HEL0_F7HEL0_MACMU_9544 and tr_A0A2K5XR64_A0A2K5XR64_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZHQ9_H0ZHQ9_TAEGU_59729 and tr_A0A093QBJ6_A0A093QBJ6_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZHQ9_H0ZHQ9_TAEGU_59729 and tr_A0A091W0M3_A0A091W0M3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1LJ22_G1LJ22_AILME_9646 and tr_A0A384C518_A0A384C518_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7NYN2_G7NYN2_MACFA_9541 and tr_A0A2K5YSV0_A0A2K5YSV0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096MPN1_A0A096MPN1_PAPAN_9555 and tr_A0A2K5KRK7_A0A2K5KRK7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MPN1_A0A096MPN1_PAPAN_9555 and tr_A0A2K6B4J0_A0A2K6B4J0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LW74_A0A2I3LW74_PAPAN_9555 and tr_A0A0D9RA24_A0A0D9RA24_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3MS05_A0A2I3MS05_PAPAN_9555 and tr_A0A2K5KTZ0_A0A2K5KTZ0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1S3MSZ9_A0A1S3MSZ9_SALSA_8030 and tr_A0A1S3MYC2_A0A1S3MYC2_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226MET6_A0A226MET6_CALSU_9009 and tr_A0A226PS21_A0A226PS21_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NDX7_A0A226NDX7_CALSU_9009 and tr_A0A226PP75_A0A226PP75_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3W3R4_A0A2U3W3R4_ODORO_9708 and tr_A0A2U3YXT5_A0A2U3YXT5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9Q643_A0A2Y9Q643_DELLE_9749 and tr_A0A383Z8I6_A0A383Z8I6_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 35 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/B2RNN3/4_raxmlng_ancestral/B2RNN3.raxml.reduced.phy Alignment comprises 1 partitions and 333 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 333 Gaps: 25.43 % Invariant sites: 0.30 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RNN3/4_raxmlng_ancestral/B2RNN3.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/B2RNN3/3_mltree/B2RNN3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 84 / 6720 [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: -151073.108866 [00:00:00 -151073.108866] Initial branch length optimization [00:00:01 -149310.172406] Model parameter optimization (eps = 0.100000) [00:00:38] Tree #1, final logLikelihood: -148815.265590 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.073277,0.555174) (0.223055,0.493254) (0.254939,0.643071) (0.448729,1.527318) 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/B2RNN3/4_raxmlng_ancestral/B2RNN3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RNN3/4_raxmlng_ancestral/B2RNN3.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RNN3/4_raxmlng_ancestral/B2RNN3.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RNN3/4_raxmlng_ancestral/B2RNN3.raxml.log Analysis started: 17-Jul-2021 08:29:41 / finished: 17-Jul-2021 08:30:23 Elapsed time: 41.578 seconds