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 15:09:20 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P36871/2_msa/P36871_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P36871/3_mltree/P36871.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P36871/4_raxmlng_ancestral/P36871 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635760 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/P36871/2_msa/P36871_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 562 sites WARNING: Sequences tr_J3KBT8_J3KBT8_COCIM_246410 and tr_A0A0J7BCP6_A0A0J7BCP6_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6Q1E8_B6Q1E8_TALMQ_441960 and tr_A0A093VQQ0_A0A093VQQ0_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WEJ3_B2WEJ3_PYRTR_426418 and tr_A0A2W1ECJ8_A0A2W1ECJ8_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3QM78_G3QM78_GORGO_9595 and tr_A0A2R9BEH7_A0A2R9BEH7_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q7SCJ9_Q7SCJ9_NEUCR_367110 and tr_G4U9B7_G4U9B7_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8N1K6_B8N1K6_ASPFN_332952 and sp_P57749_PGM_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N1K6_B8N1K6_ASPFN_332952 and tr_A0A1S9DMA3_A0A1S9DMA3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UTL8_A0A179UTL8_BLAGS_559298 and tr_C5G9X1_C5G9X1_AJEDR_559297 are exactly identical! WARNING: Sequences tr_W5PJB6_W5PJB6_SHEEP_9940 and sp_Q08DP0_PGM1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F9G360_F9G360_FUSOF_660025 and tr_N4TFA8_N4TFA8_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G360_F9G360_FUSOF_660025 and tr_A0A2H3TCK4_A0A2H3TCK4_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9G360_F9G360_FUSOF_660025 and tr_A0A2H3IAD3_A0A2H3IAD3_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9G360_F9G360_FUSOF_660025 and tr_A0A365N6I4_A0A365N6I4_GIBIN_948311 are exactly identical! WARNING: Sequences tr_A1D6P1_A1D6P1_NEOFI_331117 and tr_A0A0S7DGB8_A0A0S7DGB8_9EURO_293939 are exactly identical! WARNING: Sequences tr_A2QDM7_A2QDM7_ASPNC_425011 and tr_G3Y3N7_G3Y3N7_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QDM7_A2QDM7_ASPNC_425011 and tr_A0A319B9H2_A0A319B9H2_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7G9X6_F7G9X6_MACMU_9544 and tr_A0A0D9S732_A0A0D9S732_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7G9X6_F7G9X6_MACMU_9544 and tr_A0A2K5NU60_A0A2K5NU60_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HU87_F7HU87_MACMU_9544 and tr_A0A2K5NE29_A0A2K5NE29_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HU87_F7HU87_MACMU_9544 and tr_A0A2K6DVH8_A0A2K6DVH8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XPN8_G7XPN8_ASPKW_1033177 and tr_A0A146FCB1_A0A146FCB1_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A0A1D6GJ73_A0A1D6GJ73_MAIZE_4577 and sp_P93804_PGMC1_MAIZE_4577 are exactly identical! WARNING: Sequences tr_A0A1D6L1Y9_A0A1D6L1Y9_MAIZE_4577 and sp_P93805_PGMC2_MAIZE_4577 are exactly identical! WARNING: Sequences tr_I1PEZ3_I1PEZ3_ORYGL_4538 and tr_Q9AUQ4_Q9AUQ4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1QT43_I1QT43_ORYGL_4538 and tr_Q33AE4_Q33AE4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G2Y528_G2Y528_BOTF4_999810 and tr_M7U500_M7U500_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SF75_F2SF75_TRIRC_559305 and tr_A0A178EU71_A0A178EU71_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G7PSH2_G7PSH2_MACFA_9541 and tr_A0A2K5XKB9_A0A2K5XKB9_MANLE_9568 are exactly identical! WARNING: Sequences tr_F2PWE6_F2PWE6_TRIEC_559882 and tr_A0A059J4A0_A0A059J4A0_9EURO_1215338 are exactly identical! WARNING: Sequences tr_V2X699_V2X699_MONRO_1381753 and tr_A0A0W0EXP7_A0A0W0EXP7_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PLY2_W2PLY2_PHYPN_761204 and tr_A0A0W8CPD2_A0A0W8CPD2_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A015IW01_A0A015IW01_9GLOM_1432141 and tr_A0A2I1DY88_A0A2I1DY88_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015IW01_A0A015IW01_9GLOM_1432141 and tr_U9TJT9_U9TJT9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067EYI3_A0A067EYI3_CITSI_2711 and tr_A0A2H5NM86_A0A2H5NM86_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A078JGT8_A0A078JGT8_BRANA_3708 and tr_A0A0D3EA69_A0A0D3EA69_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094EPR6_A0A094EPR6_9PEZI_1420912 and tr_A0A2P6FGQ8_A0A2P6FGQ8_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0A2KVX0_A0A0A2KVX0_PENIT_40296 and tr_A0A0A2IMC1_A0A0A2IMC1_PENEN_27334 are exactly identical! WARNING: Sequences tr_V4W5U2_V4W5U2_9ROSI_85681 and tr_A0A2H5Q3R4_A0A2H5Q3R4_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0F0IBB1_A0A0F0IBB1_ASPPU_1403190 and tr_A0A2G7FKN7_A0A2G7FKN7_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F8VMA6_A0A0F8VMA6_9EURO_308745 and tr_A0A2T5LYM1_A0A2T5LYM1_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0N0V8J9_A0A0N0V8J9_FUSLA_179993 and tr_A0A1B8B144_A0A1B8B144_FUSPO_36050 are exactly identical! WARNING: Sequences tr_A0A0N0V8J9_A0A0N0V8J9_FUSLA_179993 and tr_A0A2L2TLH5_A0A2L2TLH5_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A0V1DC61_A0A0V1DC61_TRIBR_45882 and tr_A0A0V1PMM3_A0A0V1PMM3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DC61_A0A0V1DC61_TRIBR_45882 and tr_A0A0V0TK33_A0A0V0TK33_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A100I889_A0A100I889_ASPNG_5061 and tr_A0A1L9N7K0_A0A1L9N7K0_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A100I889_A0A100I889_ASPNG_5061 and tr_A0A317USZ0_A0A317USZ0_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A1V8UQH1_A0A1V8UQH1_9PEZI_1974281 and tr_A0A1V8T9A4_A0A1V8T9A4_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A226NGV3_A0A226NGV3_CALSU_9009 and tr_A0A226PRN3_A0A226PRN3_COLVI_9014 are exactly identical! WARNING: Duplicate sequences found: 48 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/P36871/4_raxmlng_ancestral/P36871.raxml.reduced.phy Alignment comprises 1 partitions and 562 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 562 Gaps: 3.97 % Invariant sites: 2.67 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P36871/4_raxmlng_ancestral/P36871.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/P36871/3_mltree/P36871.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 141 / 11280 [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: -186437.305273 [00:00:00 -186437.305273] Initial branch length optimization [00:00:01 -186156.527733] Model parameter optimization (eps = 0.100000) [00:00:29] Tree #1, final logLikelihood: -185859.398974 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.222768,0.269922) (0.330225,0.468497) (0.228967,1.087731) (0.218041,2.458745) 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/P36871/4_raxmlng_ancestral/P36871.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P36871/4_raxmlng_ancestral/P36871.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P36871/4_raxmlng_ancestral/P36871.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P36871/4_raxmlng_ancestral/P36871.raxml.log Analysis started: 02-Jun-2021 15:09:20 / finished: 02-Jun-2021 15:09:55 Elapsed time: 34.880 seconds