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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 27-Jul-2021 16:09:58 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/2_msa/A6NFY7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/3_mltree/A6NFY7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/4_raxmlng_ancestral/A6NFY7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1627391398 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/2_msa/A6NFY7_nogap_msa.fasta [00:00:00] Loaded alignment with 568 taxa and 115 sites WARNING: Sequences tr_J3K9Z7_J3K9Z7_COCIM_246410 and tr_A0A0J6Y172_A0A0J6Y172_COCIT_404692 are exactly identical! WARNING: Sequences tr_G2X2J1_G2X2J1_VERDV_498257 and tr_A0A0G4LDH5_A0A0G4LDH5_9PEZI_100787 are exactly identical! WARNING: Sequences tr_G2X2J1_G2X2J1_VERDV_498257 and tr_A0A0G4M7L6_A0A0G4M7L6_9PEZI_100787 are exactly identical! WARNING: Sequences tr_A0A179UFM2_A0A179UFM2_BLAGS_559298 and tr_C5GG44_C5GG44_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2R660_H2R660_PANTR_9598 and tr_A0A2R8ZEV3_A0A2R8ZEV3_PANPA_9597 are exactly identical! WARNING: Sequences tr_M4AZN8_M4AZN8_XIPMA_8083 and tr_A0A087YPX9_A0A087YPX9_POEFO_48698 are exactly identical! WARNING: Sequences tr_F6X7B7_F6X7B7_MACMU_9544 and tr_A0A0A0MVB5_A0A0A0MVB5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6X7B7_F6X7B7_MACMU_9544 and tr_A0A2K5L3U3_A0A2K5L3U3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6X7B7_F6X7B7_MACMU_9544 and tr_A0A2K6AYR1_A0A2K6AYR1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A2YTD3_A2YTD3_ORYSI_39946 and tr_A0A0E0QGQ3_A0A0E0QGQ3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2YTD3_A2YTD3_ORYSI_39946 and tr_A0A0E0AT71_A0A0E0AT71_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A2YTD3_A2YTD3_ORYSI_39946 and tr_Q6Z1L3_Q6Z1L3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F2SHD0_F2SHD0_TRIRC_559305 and tr_F2Q497_F2Q497_TRIEC_559882 are exactly identical! WARNING: Sequences tr_G3YEM3_G3YEM3_ASPNA_380704 and tr_A0A319AB55_A0A319AB55_9EURO_1450533 are exactly identical! WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_S0DNC0_S0DNC0_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_N4TN99_N4TN99_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_X0CDH2_X0CDH2_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_A0A2H3SV16_A0A2H3SV16_FUSOX_5507 are exactly identical! WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_A0A2H3I448_A0A2H3I448_FUSOX_327505 are exactly identical! WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_A0A2K0WDI3_A0A2K0WDI3_GIBNY_42673 are exactly identical! WARNING: Sequences tr_M4DKM5_M4DKM5_BRARP_51351 and tr_A0A0D3C579_A0A0D3C579_BRAOL_109376 are exactly identical! WARNING: Sequences tr_M8A8G7_M8A8G7_TRIUA_4572 and tr_A0A3B6HM86_A0A3B6HM86_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M8A8G7_M8A8G7_TRIUA_4572 and tr_A0A3B6JPE3_A0A3B6JPE3_WHEAT_4565 are exactly identical! WARNING: Sequences tr_V2XR52_V2XR52_MONRO_1381753 and tr_A0A0W0F3W1_A0A0W0F3W1_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2QPU5_W2QPU5_PHYPN_761204 and tr_W2JPF4_W2JPF4_PHYPR_4792 are exactly identical! WARNING: Sequences tr_V4T3W6_V4T3W6_9ROSI_85681 and tr_A0A2H5QIH1_A0A2H5QIH1_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2VEU1_A0A0D2VEU1_GOSRA_29730 and tr_A0A1U8KMI7_A0A1U8KMI7_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0N0DE52_A0A0N0DE52_FUSLA_179993 and tr_A0A0E0RQ37_A0A0E0RQ37_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A0N0DE52_A0A0N0DE52_FUSLA_179993 and tr_A0A1B8B3Q7_A0A1B8B3Q7_FUSPO_36050 are exactly identical! WARNING: Sequences tr_A0A0N0DE52_A0A0N0DE52_FUSLA_179993 and tr_A0A2T4H658_A0A2T4H658_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A161VLD0_A0A161VLD0_9PEZI_708197 and tr_A0A167BGN0_A0A167BGN0_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_A0A164TE16_A0A164TE16_9HOMO_1314777 and tr_A0A166DUI5_A0A166DUI5_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S4DDE5_A0A1S4DDE5_TOBAC_4097 and tr_A0A1U7XE57_A0A1U7XE57_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1F5LYJ0_A0A1F5LYJ0_9EURO_1835702 and tr_A0A1V6Q443_A0A1V6Q443_9EURO_416450 are exactly identical! WARNING: Sequences tr_A0A1L9NMH1_A0A1L9NMH1_ASPTU_767770 and tr_A0A317UPM5_A0A317UPM5_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A1V8U0E6_A0A1V8U0E6_9PEZI_1974281 and tr_A0A1V8U3F6_A0A1V8U3F6_9PEZI_1974281 are exactly identical! WARNING: Sequences tr_A0A2H3C9Q0_A0A2H3C9Q0_9AGAR_1076256 and tr_A0A284RG11_A0A284RG11_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A1U8E5C9_A0A1U8E5C9_CAPAN_4072 and tr_A0A2G3BJN4_A0A2G3BJN4_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2I2F6P8_A0A2I2F6P8_9EURO_41067 and tr_A0A2J5I304_A0A2J5I304_9EURO_482145 are exactly identical! WARNING: Sequences tr_A0A2S7PE33_A0A2S7PE33_9HELO_2070414 and tr_A0A2S7QNZ6_A0A2S7QNZ6_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2T7D5Q0_A0A2T7D5Q0_9POAL_1504633 and tr_A0A2T7D5R3_A0A2T7D5R3_9POAL_1504633 are exactly identical! WARNING: Duplicate sequences found: 41 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/4_raxmlng_ancestral/A6NFY7.raxml.reduced.phy Alignment comprises 1 partitions and 115 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 115 Gaps: 33.88 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/4_raxmlng_ancestral/A6NFY7.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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/3_mltree/A6NFY7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 29 / 2320 [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: -31197.545227 [00:00:00 -31197.545227] Initial branch length optimization [00:00:00 -30949.493776] Model parameter optimization (eps = 0.100000) [00:00:17] Tree #1, final logLikelihood: -30743.308195 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.167596,0.360055) (0.167965,0.477479) (0.420828,0.864168) (0.243611,2.035172) 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/4_raxmlng_ancestral/A6NFY7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/4_raxmlng_ancestral/A6NFY7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/4_raxmlng_ancestral/A6NFY7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NFY7/4_raxmlng_ancestral/A6NFY7.raxml.log Analysis started: 27-Jul-2021 16:09:58 / finished: 27-Jul-2021 16:10:16 Elapsed time: 18.224 seconds Consumed energy: 1.485 Wh