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 02-Jun-2021 18:24:30 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9BR39/2_msa/Q9BR39_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9BR39/3_mltree/Q9BR39.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9BR39/4_raxmlng_ancestral/Q9BR39 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647470 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/020621_run/phylogeny-snakemake/results/Q9BR39/2_msa/Q9BR39_nogap_msa.fasta [00:00:00] Loaded alignment with 996 taxa and 696 sites WARNING: Sequences tr_G3QK17_G3QK17_GORGO_9595 and sp_Q9HDC5_JPH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8QK67_A0A2J8QK67_PANTR_9598 and sp_Q96JJ6_JPH4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2RA04_H2RA04_PANTR_9598 and tr_A0A2R9C555_A0A2R9C555_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7GA58_F7GA58_MACMU_9544 and tr_A0A2K5Y1N4_A0A2K5Y1N4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GA58_F7GA58_MACMU_9544 and tr_A0A2R9AA79_A0A2R9AA79_PANPA_9597 are exactly identical! WARNING: Sequences tr_A2XB57_A2XB57_ORYSI_39946 and tr_I1P5N9_I1P5N9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2XB57_A2XB57_ORYSI_39946 and tr_A0A0D3FC85_A0A0D3FC85_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2XB57_A2XB57_ORYSI_39946 and tr_A0A0D9Z0B7_A0A0D9Z0B7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0NN08_A0A0E0NN08_ORYRU_4529 and tr_Q6KA01_Q6KA01_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0P070_A0A0E0P070_ORYRU_4529 and tr_A0A0D3FN04_A0A0D3FN04_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0P070_A0A0E0P070_ORYRU_4529 and tr_A0A0D9ZC73_A0A0D9ZC73_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_B3S2M3_B3S2M3_TRIAD_10228 and tr_A0A369SMW2_A0A369SMW2_9METZ_287889 are exactly identical! WARNING: Sequences tr_M4EEA9_M4EEA9_BRARP_51351 and tr_A0A078FEQ6_A0A078FEQ6_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4FG18_M4FG18_BRARP_51351 and tr_A0A0D3AF27_A0A0D3AF27_BRAOL_109376 are exactly identical! WARNING: Sequences tr_M7ZSB4_M7ZSB4_TRIUA_4572 and tr_A0A3B6NVK7_A0A3B6NVK7_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067EUT7_A0A067EUT7_CITSI_2711 and tr_A0A2H5PW43_A0A2H5PW43_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A096NGB3_A0A096NGB3_PAPAN_9555 and tr_A0A2K5NXK9_A0A2K5NXK9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NGB3_A0A096NGB3_PAPAN_9555 and tr_A0A2K6DT99_A0A2K6DT99_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A078GAY0_A0A078GAY0_BRANA_3708 and tr_A0A078HF44_A0A078HF44_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A0D9RTR4_A0A0D9RTR4_CHLSB_60711 and tr_A0A2K6CSV5_A0A2K6CSV5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9S225_A0A0D9S225_CHLSB_60711 and tr_A0A2K5ZBC6_A0A2K5ZBC6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0LB60_A0A0A0LB60_CUCSA_3659 and tr_A0A1S3B5X1_A0A1S3B5X1_CUCME_3656 are exactly identical! WARNING: Sequences tr_V4T1A9_V4T1A9_9ROSI_85681 and tr_A0A2H5QQG8_A0A2H5QQG8_CITUN_55188 are exactly identical! WARNING: Sequences tr_V4TCJ0_V4TCJ0_9ROSI_85681 and tr_A0A2H5NNG8_A0A2H5NNG8_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2NYI6_A0A0D2NYI6_GOSRA_29730 and tr_A0A1U8NSS3_A0A1U8NSS3_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2UVZ3_A0A0D2UVZ3_GOSRA_29730 and tr_A0A1U8J8X7_A0A1U8J8X7_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A091JK22_A0A091JK22_EGRGA_188379 and tr_A0A091UTU4_A0A091UTU4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JK22_A0A091JK22_EGRGA_188379 and tr_A0A087QY53_A0A087QY53_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JK22_A0A091JK22_EGRGA_188379 and tr_A0A091WIB7_A0A091WIB7_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JK22_A0A091JK22_EGRGA_188379 and tr_A0A0A0ATF7_A0A0A0ATF7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CJ45_A0A0V1CJ45_TRIBR_45882 and tr_A0A0V0V3A8_A0A0V0V3A8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CJ45_A0A0V1CJ45_TRIBR_45882 and tr_A0A0V0ZX47_A0A0V0ZX47_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1D8P5_A0A0V1D8P5_TRIBR_45882 and tr_A0A0V0ZTG6_A0A0V0ZTG6_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1L2N1_A0A0V1L2N1_9BILA_6335 and tr_A0A0V1FHV7_A0A0V1FHV7_TRIPS_6337 are exactly identical! WARNING: Sequences tr_A0A0V1L2N1_A0A0V1L2N1_9BILA_6335 and tr_A0A0V1NV18_A0A0V1NV18_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1L2N1_A0A0V1L2N1_9BILA_6335 and tr_A0A0V0TIN6_A0A0V0TIN6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1MJJ4_A0A0V1MJJ4_9BILA_268474 and tr_A0A0V1GZL8_A0A0V1GZL8_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V1PL97_A0A0V1PL97_9BILA_92180 and tr_A0A0V0UG16_A0A0V0UG16_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3X5R0_A0A1S3X5R0_TOBAC_4097 and tr_A0A1U7WB42_A0A1U7WB42_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4BSC9_A0A1S4BSC9_TOBAC_4097 and tr_A0A1S4CTK7_A0A1S4CTK7_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S4BZ99_A0A1S4BZ99_TOBAC_4097 and tr_A0A1U7WWE4_A0A1U7WWE4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DNX7_A0A1S4DNX7_TOBAC_4097 and tr_A0A1U7XMT0_A0A1U7XMT0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A3Q0FFS6_A0A3Q0FFS6_VIGRR_3916 and tr_A0A3Q0FIW2_A0A3Q0FIW2_VIGRR_3916 are exactly identical! WARNING: Duplicate sequences found: 43 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9BR39/4_raxmlng_ancestral/Q9BR39.raxml.reduced.phy Alignment comprises 1 partitions and 696 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 696 Gaps: 40.31 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9BR39/4_raxmlng_ancestral/Q9BR39.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/020621_run/phylogeny-snakemake/results/Q9BR39/3_mltree/Q9BR39.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 174 / 13920 [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: -261737.227822 [00:00:00 -261737.227822] Initial branch length optimization [00:00:02 -234160.791669] Model parameter optimization (eps = 0.100000) [00:01:06] Tree #1, final logLikelihood: -233027.850117 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.090443,0.613254) (0.121137,0.998280) (0.424954,0.660176) (0.363466,1.494122) 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/020621_run/phylogeny-snakemake/results/Q9BR39/4_raxmlng_ancestral/Q9BR39.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9BR39/4_raxmlng_ancestral/Q9BR39.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9BR39/4_raxmlng_ancestral/Q9BR39.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9BR39/4_raxmlng_ancestral/Q9BR39.raxml.log Analysis started: 02-Jun-2021 18:24:30 / finished: 02-Jun-2021 18:25:44 Elapsed time: 73.785 seconds Consumed energy: 5.140 Wh