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 17:59:13 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IY33/2_msa/Q8IY33_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IY33/3_mltree/Q8IY33.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IY33/4_raxmlng_ancestral/Q8IY33 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101953 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/Q8IY33/2_msa/Q8IY33_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 904 sites WARNING: Sequences tr_M3YH04_M3YH04_MUSPF_9669 and tr_A0A2Y9JJV6_A0A2Y9JJV6_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P18091_ACTN_DROME_7227 and tr_A0A1W4VEA9_A0A1W4VEA9_DROFC_30025 are exactly identical! WARNING: Sequences tr_A0A2I2ZV52_A0A2I2ZV52_GORGO_9595 and tr_F6VRJ5_F6VRJ5_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2ZV52_A0A2I2ZV52_GORGO_9595 and tr_A0A2K5N9D6_A0A2K5N9D6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2ZV52_A0A2I2ZV52_GORGO_9595 and tr_A0A2R9AQJ0_A0A2R9AQJ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R7J8_G3R7J8_GORGO_9595 and tr_A0A2I3S2C5_A0A2I3S2C5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R7J8_G3R7J8_GORGO_9595 and tr_A0A2R8ZIT5_A0A2R8ZIT5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2P675_H2P675_PONAB_9601 and sp_Q01082_SPTB2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8QB90_A0A2J8QB90_PANTR_9598 and tr_A0A2R9A0X1_A0A2R9A0X1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NGS2_A0A158NGS2_ATTCE_12957 and tr_A0A195BVX4_A0A195BVX4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NJ82_A0A158NJ82_ATTCE_12957 and tr_A0A151JNA1_A0A151JNA1_9HYME_471704 are exactly identical! WARNING: Sequences tr_F7FS44_F7FS44_MACMU_9544 and tr_A0A2I3M122_A0A2I3M122_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FS44_F7FS44_MACMU_9544 and tr_A0A2K5P4S5_A0A2K5P4S5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FS44_F7FS44_MACMU_9544 and tr_A0A2K6CPD6_A0A2K6CPD6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FS44_F7FS44_MACMU_9544 and tr_A0A2K5XT52_A0A2K5XT52_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6WKC6_F6WKC6_CALJA_9483 and tr_G7NWN5_G7NWN5_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7P3P2_G7P3P2_MACFA_9541 and tr_A0A2K5LZI1_A0A2K5LZI1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P3P2_G7P3P2_MACFA_9541 and tr_A0A2K6D6I7_A0A2K6D6I7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PQP9_G7PQP9_MACFA_9541 and tr_A0A2K5P755_A0A2K5P755_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PQP9_G7PQP9_MACFA_9541 and tr_A0A2K6CGD9_A0A2K6CGD9_MACNE_9545 are exactly identical! WARNING: Sequences sp_F1MF74_MICA2_BOVIN_9913 and tr_H9GW33_H9GW33_BOVIN_9913 are exactly identical! WARNING: Sequences tr_L0P961_L0P961_PNEJ8_1209962 and tr_A0A0W4ZTP2_A0A0W4ZTP2_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_U3K9Y0_U3K9Y0_FICAL_59894 and tr_A0A218UIK1_A0A218UIK1_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A096NVY8_A0A096NVY8_PAPAN_9555 and tr_A0A2K5LG92_A0A2K5LG92_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0L7QV59_A0A0L7QV59_9HYME_597456 and tr_A0A2A3EMK6_A0A2A3EMK6_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A091ILB0_A0A091ILB0_CALAN_9244 and tr_A0A1V4IHD4_A0A1V4IHD4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CWE6_A0A0V1CWE6_TRIBR_45882 and tr_A0A0V0X125_A0A0V0X125_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CWE6_A0A0V1CWE6_TRIBR_45882 and tr_A0A0V0VNJ7_A0A0V0VNJ7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CWE6_A0A0V1CWE6_TRIBR_45882 and tr_A0A0V1KXT2_A0A0V1KXT2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CWE6_A0A0V1CWE6_TRIBR_45882 and tr_A0A0V0ZNF3_A0A0V0ZNF3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CWE6_A0A0V1CWE6_TRIBR_45882 and tr_A0A0V0TZT7_A0A0V0TZT7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D9G3_A0A0V1D9G3_TRIBR_45882 and tr_A0A0V1A0K1_A0A0V1A0K1_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1D9G3_A0A0V1D9G3_TRIBR_45882 and tr_A0A0V0U100_A0A0V0U100_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0X058_A0A0V0X058_9BILA_92179 and tr_A0A0V1L6U6_A0A0V1L6U6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0V954_A0A0V0V954_9BILA_181606 and tr_A0A0V0TM60_A0A0V0TM60_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0VWR7_A0A0V0VWR7_9BILA_181606 and tr_A0A0V1PGW4_A0A0V1PGW4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1MMA7_A0A0V1MMA7_9BILA_268474 and tr_A0A0V1HR16_A0A0V1HR16_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A226MIJ8_A0A226MIJ8_CALSU_9009 and tr_A0A226P2N7_A0A226P2N7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2A2J3V7_A0A2A2J3V7_9BILA_2018661 and tr_A0A2A2LIT2_A0A2A2LIT2_9BILA_2018661 are exactly identical! WARNING: Sequences tr_A0A2D0Q8N2_A0A2D0Q8N2_ICTPU_7998 and tr_A0A2D0QCE0_A0A2D0QCE0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5MSA6_A0A2K5MSA6_CERAT_9531 and tr_A0A2K6C4H3_A0A2K6C4H3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5MSA6_A0A2K5MSA6_CERAT_9531 and tr_A0A2K5ZBW9_A0A2K5ZBW9_MANLE_9568 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/Q8IY33/4_raxmlng_ancestral/Q8IY33.raxml.reduced.phy Alignment comprises 1 partitions and 904 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 904 Gaps: 39.29 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IY33/4_raxmlng_ancestral/Q8IY33.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/Q8IY33/3_mltree/Q8IY33.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 226 / 18080 [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: -329016.191373 [00:00:00 -329016.191373] Initial branch length optimization [00:00:02 -310340.723137] Model parameter optimization (eps = 0.100000) [00:01:10] Tree #1, final logLikelihood: -309464.289356 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.077043,0.240764) (0.046827,0.248566) (0.247730,0.539829) (0.628400,1.330490) 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/Q8IY33/4_raxmlng_ancestral/Q8IY33.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IY33/4_raxmlng_ancestral/Q8IY33.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IY33/4_raxmlng_ancestral/Q8IY33.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IY33/4_raxmlng_ancestral/Q8IY33.raxml.log Analysis started: 12-Jul-2021 17:59:13 / finished: 12-Jul-2021 18:00:32 Elapsed time: 79.192 seconds Consumed energy: 5.978 Wh