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 02-Jun-2021 15:22:20 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P02675/2_msa/P02675_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P02675/3_mltree/P02675.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P02675/4_raxmlng_ancestral/P02675 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622636540 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/P02675/2_msa/P02675_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 491 sites WARNING: Sequences tr_A0A140LG86_A0A140LG86_DANRE_7955 and tr_A0A2R8QBE6_A0A2R8QBE6_DANRE_7955 are exactly identical! WARNING: Sequences tr_E1BV78_E1BV78_CHICK_9031 and tr_G1MRP5_G1MRP5_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q9R045_ANGL2_MOUSE_10090 and tr_G3V862_G3V862_RAT_10116 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_K7BRA2_K7BRA2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_H0WNX1_H0WNX1_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_F7GXP6_F7GXP6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_U3D4B8_U3D4B8_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_G8F2W1_G8F2W1_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A096P212_A0A096P212_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A0D9RMK9_A0A0D9RMK9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A1U7T7C7_A0A1U7T7C7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A2K5KRS0_A0A2K5KRS0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A2K6BM30_A0A2K6BM30_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A2K5Z7E9_A0A2K5Z7E9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QT57_G3QT57_GORGO_9595 and tr_A0A2R8ZSV1_A0A2R8ZSV1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8UC26_A0A2J8UC26_PONAB_9601 and tr_H2Q0P0_H2Q0P0_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8UC26_A0A2J8UC26_PONAB_9601 and tr_H9EU04_H9EU04_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2J8UC26_A0A2J8UC26_PONAB_9601 and tr_A0A0D9RI18_A0A0D9RI18_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8UC26_A0A2J8UC26_PONAB_9601 and tr_A0A2K5NMC3_A0A2K5NMC3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2J8UC26_A0A2J8UC26_PONAB_9601 and tr_A0A2K5ZAF3_A0A2K5ZAF3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2J8UC26_A0A2J8UC26_PONAB_9601 and tr_A0A2R9A861_A0A2R9A861_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T2M5_A0A2I3T2M5_PANTR_9598 and tr_A0A2R9C4Y3_A0A2R9C4Y3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QQB4_H2QQB4_PANTR_9598 and tr_A0A2R9AN20_A0A2R9AN20_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QDY3_A0A1D5QDY3_MACMU_9544 and tr_A0A2K6D626_A0A2K6D626_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UZ20_F6UZ20_MACMU_9544 and tr_G7P6F9_G7P6F9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6UZ20_F6UZ20_MACMU_9544 and tr_A0A2K6D4Y0_A0A2K6D4Y0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UZ87_F6UZ87_MACMU_9544 and tr_G7P6F7_G7P6F7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6X2C2_F6X2C2_MACMU_9544 and tr_A0A2K6D7M0_A0A2K6D7M0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HKS2_F7HKS2_MACMU_9544 and tr_A0A2K6BNT8_A0A2K6BNT8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HQR6_F7HQR6_MACMU_9544 and tr_A0A096MX05_A0A096MX05_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HQR6_F7HQR6_MACMU_9544 and tr_A0A2K6DZQ6_A0A2K6DZQ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HQR6_F7HQR6_MACMU_9544 and tr_A0A2K6AAY2_A0A2K6AAY2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7P6F8_G7P6F8_MACFA_9541 and tr_A0A2K6CDF6_A0A2K6CDF6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MP49_A0A096MP49_PAPAN_9555 and tr_A0A2K6AHI8_A0A2K6AHI8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NXK6_A0A096NXK6_PAPAN_9555 and tr_A0A2K5YQP3_A0A2K5YQP3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091IKF7_A0A091IKF7_EGRGA_188379 and tr_A0A091W1Z5_A0A091W1Z5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IKF7_A0A091IKF7_EGRGA_188379 and tr_A0A0A0B078_A0A0A0B078_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091IKF7_A0A091IKF7_EGRGA_188379 and tr_A0A2I0MC32_A0A2I0MC32_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A226N2D7_A0A226N2D7_CALSU_9009 and tr_A0A226NXC5_A0A226NXC5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NA62_A0A226NA62_CALSU_9009 and tr_A0A226PC07_A0A226PC07_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NNT6_A0A226NNT6_CALSU_9009 and tr_A0A226P2C0_A0A226P2C0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2Y9J9L8_A0A2Y9J9L8_ENHLU_391180 and tr_A0A384CQ75_A0A384CQ75_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 42 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/P02675/4_raxmlng_ancestral/P02675.raxml.reduced.phy Alignment comprises 1 partitions and 491 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 491 Gaps: 34.59 % Invariant sites: 2.24 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P02675/4_raxmlng_ancestral/P02675.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/P02675/3_mltree/P02675.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 123 / 9840 [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: -163098.721330 [00:00:00 -163098.721330] Initial branch length optimization [00:00:01 -161961.715328] Model parameter optimization (eps = 0.100000) [00:00:26] Tree #1, final logLikelihood: -161875.982557 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.082497,0.096248) (0.139065,0.335051) (0.369515,0.702778) (0.408924,1.677035) 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/P02675/4_raxmlng_ancestral/P02675.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P02675/4_raxmlng_ancestral/P02675.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P02675/4_raxmlng_ancestral/P02675.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P02675/4_raxmlng_ancestral/P02675.raxml.log Analysis started: 02-Jun-2021 15:22:20 / finished: 02-Jun-2021 15:22:52 Elapsed time: 31.297 seconds