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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 12-Jul-2021 17:26:58 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEG5/2_msa/Q8NEG5_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEG5/3_mltree/Q8NEG5.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEG5/4_raxmlng_ancestral/Q8NEG5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100018 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/Q8NEG5/2_msa/Q8NEG5_nogap_msa.fasta [00:00:00] Loaded alignment with 867 taxa and 633 sites WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_G3QW07_G3QW07_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and sp_Q5RCV8_RNF13_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_H2QNK4_H2QNK4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and sp_O43567_RNF13_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_H9ELX5_H9ELX5_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_G7NZM7_G7NZM7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_A0A096MS08_A0A096MS08_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_A0A0D9RGK1_A0A0D9RGK1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_A0A2K6A6Z9_A0A2K6A6Z9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_A0A2R9BEY4_A0A2R9BEY4_PANPA_9597 are exactly identical! WARNING: Sequences tr_B2W107_B2W107_PYRTR_426418 and tr_A0A317AR60_A0A317AR60_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8NBD4_B8NBD4_ASPFN_332952 and tr_A0A1S9DDC6_A0A1S9DDC6_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0GBF2_A0A0E0GBF2_ORYNI_4536 and tr_Q6ZHC6_Q6ZHC6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0GLS6_A0A0E0GLS6_ORYNI_4536 and tr_A2XG70_A2XG70_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GLS6_A0A0E0GLS6_ORYNI_4536 and tr_A0A0D9Z6M0_A0A0D9Z6M0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A2XR03_A2XR03_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_I1PJL7_I1PJL7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0E0P6A8_A0A0E0P6A8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0D3FTC8_A0A0D3FTC8_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0D9ZHS7_A0A0D9ZHS7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_Q7XT61_Q7XT61_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0HM21_A0A0E0HM21_ORYNI_4536 and tr_A2YA79_A2YA79_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HM21_A0A0E0HM21_ORYNI_4536 and tr_A0A0E0PUK3_A0A0E0PUK3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HM21_A0A0E0HM21_ORYNI_4536 and tr_A0A0D3GDQ9_A0A0D3GDQ9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_F6XH39_F6XH39_MACMU_9544 and tr_G7PL01_G7PL01_MACFA_9541 are exactly identical! WARNING: Sequences tr_I1PAW6_I1PAW6_ORYGL_4538 and tr_A0A0D3FHY2_A0A0D3FHY2_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1PYP0_I1PYP0_ORYGL_4538 and tr_A0A0D3GBQ9_A0A0D3GBQ9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1Q090_I1Q090_ORYGL_4538 and tr_B7EH89_B7EH89_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0PSA9_A0A0E0PSA9_ORYRU_4529 and tr_Q5VME8_Q5VME8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0R0M7_A0A0E0R0M7_ORYRU_4529 and tr_Q7XD81_Q7XD81_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0RCW8_A0A0E0RCW8_ORYRU_4529 and tr_Q2QYK7_Q2QYK7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_M4CV30_M4CV30_BRARP_51351 and tr_A0A078IDP9_A0A078IDP9_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4DMJ7_M4DMJ7_BRARP_51351 and tr_A0A078ICW1_A0A078ICW1_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2R565_W2R565_PHYPN_761204 and tr_A0A0W8D2M4_A0A0W8D2M4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A015IC27_A0A015IC27_9GLOM_1432141 and tr_A0A2H5SSM0_A0A2H5SSM0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015JK86_A0A015JK86_9GLOM_1432141 and tr_A0A2H5SMM8_A0A2H5SMM8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0D2N2E2_A0A0D2N2E2_GOSRA_29730 and tr_A0A1U8P985_A0A1U8P985_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0A1P7P4_A0A0A1P7P4_9FUNG_58291 and tr_A0A367K0F7_A0A367K0F7_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1PBD2_A0A0A1PBD2_9FUNG_58291 and tr_A0A367J3M1_A0A367J3M1_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A1S3XSM7_A0A1S3XSM7_TOBAC_4097 and tr_A0A1U7W449_A0A1U7W449_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4B1L8_A0A1S4B1L8_TOBAC_4097 and tr_A0A1U7XM44_A0A1U7XM44_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3VT89_A0A1S3VT89_VIGRR_3916 and tr_A0A3Q0EIW6_A0A3Q0EIW6_VIGRR_3916 are exactly identical! WARNING: Duplicate sequences found: 42 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/Q8NEG5/4_raxmlng_ancestral/Q8NEG5.raxml.reduced.phy Alignment comprises 1 partitions and 633 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 633 Gaps: 63.25 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEG5/4_raxmlng_ancestral/Q8NEG5.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/Q8NEG5/3_mltree/Q8NEG5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 159 / 12720 [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: -238039.855976 [00:00:00 -238039.855976] Initial branch length optimization [00:00:02 -216286.425174] Model parameter optimization (eps = 0.100000) [00:00:47] Tree #1, final logLikelihood: -215694.976293 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.059286,0.212451) (0.051794,0.352956) (0.342112,0.738661) (0.546809,1.310183) 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/Q8NEG5/4_raxmlng_ancestral/Q8NEG5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEG5/4_raxmlng_ancestral/Q8NEG5.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEG5/4_raxmlng_ancestral/Q8NEG5.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8NEG5/4_raxmlng_ancestral/Q8NEG5.raxml.log Analysis started: 12-Jul-2021 17:26:58 / finished: 12-Jul-2021 17:27:51 Elapsed time: 52.674 seconds Consumed energy: 3.213 Wh