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 03-Jun-2021 02:05:47 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12879/2_msa/Q12879_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12879/3_mltree/Q12879.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12879/4_raxmlng_ancestral/Q12879 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675147 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/Q12879/2_msa/Q12879_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1464 sites WARNING: Sequences sp_Q9Z2W9_GRIA3_MOUSE_10090 and tr_G7Q3M1_G7Q3M1_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q9Z2W9_GRIA3_MOUSE_10090 and tr_A0A1U7QQ36_A0A1U7QQ36_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q9Z2W9_GRIA3_MOUSE_10090 and tr_A0A2K5MNX8_A0A2K5MNX8_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q9Z2W9_GRIA3_MOUSE_10090 and tr_A0A2R8ZQ00_A0A2R8ZQ00_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_A0A2I2Z6L3_A0A2I2Z6L3_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_C7G3L5_C7G3L5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and sp_Q13002_GRIK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_H9EM65_H9EM65_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_F7IBF1_F7IBF1_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_A0A2K5LJ69_A0A2K5LJ69_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_A0A2K6BKA4_A0A2K6BKA4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1PBG8_G1PBG8_MYOLU_59463 and tr_F6VNJ0_F6VNJ0_HORSE_9796 are exactly identical! WARNING: Sequences tr_G3R3A9_G3R3A9_GORGO_9595 and tr_H2NGN9_H2NGN9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R3A9_G3R3A9_GORGO_9595 and sp_Q13224_NMDE2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8WWH6_A0A2J8WWH6_PONAB_9601 and sp_P42263_GRIA3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8WWH6_A0A2J8WWH6_PONAB_9601 and tr_A0A096N5U4_A0A096N5U4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8WWH6_A0A2J8WWH6_PONAB_9601 and tr_A0A2K6C368_A0A2K6C368_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1SKJ0_G1SKJ0_RABIT_9986 and tr_G3TGC2_G3TGC2_LOXAF_9785 are exactly identical! WARNING: Sequences tr_A0A2I3T979_A0A2I3T979_PANTR_9598 and tr_A0A2I3MXB9_A0A2I3MXB9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3T979_A0A2I3T979_PANTR_9598 and tr_A0A2K5M9E6_A0A2K5M9E6_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2Q5I0_H2Q5I0_PANTR_9598 and tr_A0A2R8ZSD1_A0A2R8ZSD1_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5PVI2_W5PVI2_SHEEP_9940 and tr_A0A2U4CHR8_A0A2U4CHR8_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5PVI2_W5PVI2_SHEEP_9940 and tr_A0A2Y9MEW1_A0A2Y9MEW1_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5PVI2_W5PVI2_SHEEP_9940 and tr_A0A2Y9SYW0_A0A2Y9SYW0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A158NUK3_A0A158NUK3_ATTCE_12957 and tr_A0A195BE52_A0A195BE52_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6T8S6_F6T8S6_MACMU_9544 and tr_G7PJX2_G7PJX2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6T8S6_F6T8S6_MACMU_9544 and tr_A0A2K6BQ06_A0A2K6BQ06_MACNE_9545 are exactly identical! WARNING: Sequences tr_F1RYR0_F1RYR0_PIG_9823 and tr_L5JKX4_L5JKX4_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1M8E3_G1M8E3_AILME_9646 and tr_A0A2I2U7P0_A0A2I2U7P0_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1M8E3_G1M8E3_AILME_9646 and tr_A0A2U3VXH1_A0A2U3VXH1_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1MG21_F1MG21_BOVIN_9913 and tr_A0A337S2R5_A0A337S2R5_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1MG21_F1MG21_BOVIN_9913 and tr_A0A2Y9L356_A0A2Y9L356_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F1MG21_F1MG21_BOVIN_9913 and tr_A0A384D8V4_A0A384D8V4_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A096NW97_A0A096NW97_PAPAN_9555 and tr_A0A2K5KMZ5_A0A2K5KMZ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RQB5_A0A0D9RQB5_CHLSB_60711 and tr_A0A1U7TEY8_A0A1U7TEY8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A091JB59_A0A091JB59_EGRGA_188379 and tr_A0A091VM91_A0A091VM91_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JB59_A0A091JB59_EGRGA_188379 and tr_A0A087RCM9_A0A087RCM9_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JB59_A0A091JB59_EGRGA_188379 and tr_A0A0A0A7T4_A0A0A0A7T4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091W2J7_A0A091W2J7_NIPNI_128390 and tr_A0A087QLX8_A0A087QLX8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1S3S493_A0A1S3S493_SALSA_8030 and tr_A0A060YW65_A0A060YW65_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1I7TSS1_A0A1I7TSS1_9PELO_1561998 and tr_A0A1I7TSS3_A0A1I7TSS3_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A226MYG0_A0A226MYG0_CALSU_9009 and tr_A0A226P0E8_A0A226P0E8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MYG5_A0A226MYG5_CALSU_9009 and tr_A0A226P111_A0A226P111_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NGI4_A0A226NGI4_CALSU_9009 and tr_A0A226PL05_A0A226PL05_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2Y9LHC8_A0A2Y9LHC8_DELLE_9749 and tr_A0A2Y9SCV8_A0A2Y9SCV8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9LHC8_A0A2Y9LHC8_DELLE_9749 and tr_A0A383Z3N2_A0A383Z3N2_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 46 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/Q12879/4_raxmlng_ancestral/Q12879.raxml.reduced.phy Alignment comprises 1 partitions and 1464 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1464 Gaps: 46.69 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12879/4_raxmlng_ancestral/Q12879.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/Q12879/3_mltree/Q12879.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 366 / 29280 [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: -328062.740790 [00:00:00 -328062.740790] Initial branch length optimization [00:00:05 -323297.885795] Model parameter optimization (eps = 0.100000) [00:03:23] Tree #1, final logLikelihood: -321807.061818 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.115867,0.340857) (0.071935,0.402234) (0.351287,0.586313) (0.460911,1.574287) 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/Q12879/4_raxmlng_ancestral/Q12879.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12879/4_raxmlng_ancestral/Q12879.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12879/4_raxmlng_ancestral/Q12879.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12879/4_raxmlng_ancestral/Q12879.raxml.log Analysis started: 03-Jun-2021 02:05:47 / finished: 03-Jun-2021 02:09:26 Elapsed time: 218.482 seconds Consumed energy: 14.839 Wh