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 12-Jul-2021 18:12:33 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/2_msa/P07954_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/3_mltree/P07954.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/4_raxmlng_ancestral/P07954 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102753 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/P07954/2_msa/P07954_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 510 sites WARNING: Sequences tr_Q9W3X6_Q9W3X6_DROME_7227 and tr_B4I081_B4I081_DROSE_7238 are exactly identical! WARNING: Sequences tr_B6Q2H4_B6Q2H4_TALMQ_441960 and tr_A0A093VGK3_A0A093VGK3_TALMA_1077442 are exactly identical! WARNING: Sequences tr_Q7S3Z6_Q7S3Z6_NEUCR_367110 and tr_G4U936_G4U936_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B5DPI9_B5DPI9_DROPS_46245 and tr_B4GRX7_B4GRX7_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A179ULD3_A0A179ULD3_BLAGS_559298 and tr_C5GAL1_C5GAL1_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_A0A0D2XGP1_A0A0D2XGP1_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_N4TRV2_N4TRV2_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_X0CYB1_X0CYB1_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_A0A2H3TPD6_A0A2H3TPD6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_A0A2H3H0N6_A0A2H3H0N6_FUSOX_327505 are exactly identical! WARNING: Sequences tr_C6HT95_C6HT95_AJECH_544712 and tr_F0UT08_F0UT08_AJEC8_544711 are exactly identical! WARNING: Sequences tr_Q2U6Q8_Q2U6Q8_ASPOR_510516 and tr_A0A1S9D9I7_A0A1S9D9I7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0GM46_A0A0E0GM46_ORYNI_4536 and tr_I1PB46_I1PB46_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GM46_A0A0E0GM46_ORYNI_4536 and tr_A0A0E0D075_A0A0E0D075_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GM46_A0A0E0GM46_ORYNI_4536 and tr_A0A0E0NUR8_A0A0E0NUR8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GM46_A0A0E0GM46_ORYNI_4536 and tr_Q10LR5_Q10LR5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_E3MWG9_E3MWG9_CAERE_31234 and tr_A0A261C7W2_A0A261C7W2_9PELO_1503980 are exactly identical! WARNING: Sequences tr_G3XW87_G3XW87_ASPNA_380704 and tr_A0A318ZZ73_A0A318ZZ73_9EURO_1450533 are exactly identical! WARNING: Sequences tr_M7YQ73_M7YQ73_TRIUA_4572 and tr_A0A0C4BJJ8_A0A0C4BJJ8_WHEAT_4565 are exactly identical! WARNING: Sequences tr_W2Q158_W2Q158_PHYPN_761204 and tr_A0A0W8D095_A0A0W8D095_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2Q158_W2Q158_PHYPN_761204 and tr_W2IPS7_W2IPS7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A010QVN6_A0A010QVN6_9PEZI_1445577 and tr_A0A135UKN0_A0A135UKN0_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_A0A067HGD8_A0A067HGD8_CITSI_2711 and tr_V4VWH7_V4VWH7_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A094GDC5_A0A094GDC5_9PEZI_1420912 and tr_A0A1B8GDP3_A0A1B8GDP3_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0B4I4R3_A0A0B4I4R3_METMF_1276143 and tr_A0A0D9NPK1_A0A0D9NPK1_METAN_1291518 are exactly identical! WARNING: Sequences tr_A0A0F8X4G0_A0A0F8X4G0_9EURO_308745 and tr_A0A2T5LRI6_A0A2T5LRI6_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V1DDM5_A0A0V1DDM5_TRIBR_45882 and tr_A0A0V0VTS2_A0A0V0VTS2_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DDM5_A0A0V1DDM5_TRIBR_45882 and tr_A0A0V1AF06_A0A0V1AF06_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DDM5_A0A0V1DDM5_TRIBR_45882 and tr_A0A0V0UG90_A0A0V0UG90_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0X6T1_A0A0V0X6T1_9BILA_92179 and tr_A0A0V1LTE2_A0A0V1LTE2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A100IQV6_A0A100IQV6_ASPNG_5061 and tr_A0A1L9MTC8_A0A1L9MTC8_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A146EYW8_A0A146EYW8_9EURO_1069201 and tr_A0A317VSG9_A0A317VSG9_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A1S3DLZ8_A0A1S3DLZ8_DIACI_121845 and tr_A0A3Q0JIY5_A0A3Q0JIY5_DIACI_121845 are exactly identical! WARNING: Sequences tr_A0A1S3YK19_A0A1S3YK19_TOBAC_4097 and tr_A0A1U7YIG2_A0A1U7YIG2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A226NFE8_A0A226NFE8_CALSU_9009 and tr_A0A226P9U8_A0A226P9U8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2S7NSM0_A0A2S7NSM0_9HELO_2070414 and tr_A0A2S7QT00_A0A2S7QT00_9HELO_2070412 are exactly identical! WARNING: Duplicate sequences found: 36 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/P07954/4_raxmlng_ancestral/P07954.raxml.reduced.phy Alignment comprises 1 partitions and 510 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 510 Gaps: 7.35 % Invariant sites: 1.18 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/4_raxmlng_ancestral/P07954.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/P07954/3_mltree/P07954.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 128 / 10240 [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: -162298.274451 [00:00:00 -162298.274451] Initial branch length optimization [00:00:01 -160438.075575] Model parameter optimization (eps = 0.100000) [00:00:23] Tree #1, final logLikelihood: -160184.062313 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.333758,0.243791) (0.265165,0.503455) (0.200066,1.048909) (0.201010,2.861957) 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/P07954/4_raxmlng_ancestral/P07954.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/4_raxmlng_ancestral/P07954.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/4_raxmlng_ancestral/P07954.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/4_raxmlng_ancestral/P07954.raxml.log Analysis started: 12-Jul-2021 18:12:33 / finished: 12-Jul-2021 18:13:01 Elapsed time: 28.218 seconds Consumed energy: 1.289 Wh