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 13:47:50 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55809/2_msa/P55809_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55809/3_mltree/P55809.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55809/4_raxmlng_ancestral/P55809 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803670 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/P55809/2_msa/P55809_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 520 sites WARNING: Sequences tr_J3KJX5_J3KJX5_COCIM_246410 and tr_E9DJJ3_E9DJJ3_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KJX5_J3KJX5_COCIM_246410 and tr_A0A0J6Y560_A0A0J6Y560_COCIT_404692 are exactly identical! WARNING: Sequences tr_B8N3H1_B8N3H1_ASPFN_332952 and tr_A0A1S9DM76_A0A1S9DM76_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NS30_B8NS30_ASPFN_332952 and tr_Q2UUS6_Q2UUS6_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NS30_B8NS30_ASPFN_332952 and tr_A0A1S9D5P1_A0A1S9D5P1_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UAY7_A0A179UAY7_BLAGS_559298 and tr_C5GXB7_C5GXB7_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FG69_F9FG69_FUSOF_660025 and tr_A0A0D2XVT2_A0A0D2XVT2_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FG69_F9FG69_FUSOF_660025 and tr_N4UHM8_N4UHM8_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FG69_F9FG69_FUSOF_660025 and tr_X0CTY4_X0CTY4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FG69_F9FG69_FUSOF_660025 and tr_A0A2H3SZP2_A0A2H3SZP2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FG69_F9FG69_FUSOF_660025 and tr_A0A2H3HFN6_A0A2H3HFN6_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A2Q843_A2Q843_ASPNC_425011 and tr_A0A319AZJ4_A0A319AZJ4_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A2QLI6_A2QLI6_ASPNC_425011 and tr_G3YG39_G3YG39_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QLI6_A2QLI6_ASPNC_425011 and tr_A0A318ZYF8_A0A318ZYF8_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XM69_G7XM69_ASPKW_1033177 and tr_A0A146F9X5_A0A146F9X5_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XP23_G7XP23_ASPKW_1033177 and tr_A0A100I3T3_A0A100I3T3_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XP23_G7XP23_ASPKW_1033177 and tr_A0A146FQ90_A0A146FQ90_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XP23_G7XP23_ASPKW_1033177 and tr_A0A1L9ND78_A0A1L9ND78_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XP23_G7XP23_ASPKW_1033177 and tr_A0A317WG54_A0A317WG54_9EURO_1448314 are exactly identical! WARNING: Sequences tr_G2YBG9_G2YBG9_BOTF4_999810 and tr_M7ULE6_M7ULE6_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_E3NHC9_E3NHC9_CAERE_31234 and tr_A0A261CEP7_A0A261CEP7_9PELO_1503980 are exactly identical! WARNING: Sequences tr_F2SEQ5_F2SEQ5_TRIRC_559305 and tr_A0A178EUD3_A0A178EUD3_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G3XTF9_G3XTF9_ASPNA_380704 and tr_A0A319BU02_A0A319BU02_9EURO_1450533 are exactly identical! WARNING: Sequences tr_W7MFR7_W7MFR7_GIBM7_334819 and tr_S0E117_S0E117_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_W7MFR7_W7MFR7_GIBM7_334819 and tr_A0A2K0WQ77_A0A2K0WQ77_GIBNY_42673 are exactly identical! WARNING: Sequences tr_W7MFR7_W7MFR7_GIBM7_334819 and tr_A0A365N2Q0_A0A365N2Q0_GIBIN_948311 are exactly identical! WARNING: Sequences tr_F2PIS2_F2PIS2_TRIEC_559882 and tr_A0A059J2Y0_A0A059J2Y0_9EURO_1215338 are exactly identical! WARNING: Sequences tr_W2QI75_W2QI75_PHYPN_761204 and tr_A0A0W8CCZ0_A0A0W8CCZ0_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QI75_W2QI75_PHYPN_761204 and tr_W2LMK1_W2LMK1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A2I3MA25_A0A2I3MA25_PAPAN_9555 and tr_A0A2K6DXW1_A0A2K6DXW1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A094GU23_A0A094GU23_9PEZI_1420912 and tr_A0A1B8GBU4_A0A1B8GBU4_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0A2KFQ0_A0A0A2KFQ0_PENIT_40296 and tr_A0A0A2J5B1_A0A0A2J5B1_PENEN_27334 are exactly identical! WARNING: Sequences tr_A0A0F0IBX0_A0A0F0IBX0_ASPPU_1403190 and tr_A0A2G7G3B6_A0A2G7G3B6_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F8TY44_A0A0F8TY44_9EURO_308745 and tr_A0A2T5LWD3_A0A2T5LWD3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A226MN81_A0A226MN81_CALSU_9009 and tr_A0A226PAM5_A0A226PAM5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3T5L7_A0A2H3T5L7_FUSOX_5507 and tr_A0A2K0WSD5_A0A2K0WSD5_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A319CIH9_A0A319CIH9_9EURO_1448315 and tr_A0A2V5IQ49_A0A2V5IQ49_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A2V5IIH3_A0A2V5IIH3_9EURO_1450541 and tr_A0A2V5H6Y8_A0A2V5H6Y8_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 38 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/P55809/4_raxmlng_ancestral/P55809.raxml.reduced.phy Alignment comprises 1 partitions and 520 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 520 Gaps: 5.64 % Invariant sites: 2.12 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55809/4_raxmlng_ancestral/P55809.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/P55809/3_mltree/P55809.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 130 / 10400 [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: -180618.234469 [00:00:00 -180618.234469] Initial branch length optimization [00:00:01 -180368.391423] Model parameter optimization (eps = 0.100000) [00:00:27] Tree #1, final logLikelihood: -179817.018528 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.284263,0.264201) (0.280139,0.391458) (0.229091,1.079137) (0.206508,2.750569) 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/P55809/4_raxmlng_ancestral/P55809.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55809/4_raxmlng_ancestral/P55809.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55809/4_raxmlng_ancestral/P55809.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P55809/4_raxmlng_ancestral/P55809.raxml.log Analysis started: 04-Jun-2021 13:47:50 / finished: 04-Jun-2021 13:48:21 Elapsed time: 31.745 seconds