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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 19-Jun-2021 20:51:01 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/2_msa/Q6ZUT3_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/3_mltree/Q6ZUT3.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/4_raxmlng_ancestral/Q6ZUT3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624125061 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/2_msa/Q6ZUT3_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 714 sites WARNING: Sequences tr_B4QW64_B4QW64_DROSI_7240 and tr_B4I3U6_B4I3U6_DROSE_7238 are exactly identical! WARNING: Sequences sp_F1P065_FARP1_CHICK_9031 and tr_R4GFM0_R4GFM0_CHICK_9031 are exactly identical! WARNING: Sequences tr_G3QKS3_G3QKS3_GORGO_9595 and tr_H2QIM7_H2QIM7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QKS3_G3QKS3_GORGO_9595 and sp_P29074_PTN4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and tr_H2QTQ8_H2QTQ8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and sp_O43491_E41L2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and tr_A0A2R9A1P9_A0A2R9A1P9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2P1T2_H2P1T2_PONAB_9601 and sp_Q9H4G0_E41L1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q28Z97_Q28Z97_DROPS_46245 and tr_B4GI25_B4GI25_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3RMK9_A0A2I3RMK9_PANTR_9598 and tr_A0A2R9AYJ0_A0A2R9AYJ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8JCK6_A0A2J8JCK6_PANTR_9598 and tr_A0A2R9BLM6_A0A2R9BLM6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8M965_A0A2J8M965_PANTR_9598 and tr_A0A2R8ZCI4_A0A2R8ZCI4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QE82_H2QE82_PANTR_9598 and tr_A0A2R9AJB0_A0A2R9AJB0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NJY3_A0A158NJY3_ATTCE_12957 and tr_F4WIK9_F4WIK9_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NTJ5_A0A158NTJ5_ATTCE_12957 and tr_F4WQV9_F4WQV9_ACREC_103372 are exactly identical! WARNING: Sequences tr_F6UAX5_F6UAX5_MACMU_9544 and tr_A0A0D9RCE7_A0A0D9RCE7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WEM9_F6WEM9_MACMU_9544 and tr_G8F3Y8_G8F3Y8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WEM9_F6WEM9_MACMU_9544 and tr_A0A2K5LAS1_A0A2K5LAS1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_G7PN58_G7PN58_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A096MX43_A0A096MX43_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A0D9RVP8_A0A0D9RVP8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A2K6CIJ0_A0A2K6CIJ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A2K5ZW56_A0A2K5ZW56_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7BWK5_F7BWK5_MACMU_9544 and tr_G7P362_G7P362_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NKD7_G7NKD7_MACMU_9544 and tr_G7PWE9_G7PWE9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NKD7_G7NKD7_MACMU_9544 and tr_A0A2I3MPL2_A0A2I3MPL2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NKD7_G7NKD7_MACMU_9544 and tr_A0A0D9RYC3_A0A0D9RYC3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7NKD7_G7NKD7_MACMU_9544 and tr_A0A2K5MF59_A0A2K5MF59_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PVM2_G7PVM2_MACFA_9541 and tr_A0A096MYU4_A0A096MYU4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PVM2_G7PVM2_MACFA_9541 and tr_A0A2K6B6S0_A0A2K6B6S0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3M5V1_A0A2I3M5V1_PAPAN_9555 and tr_A0A2K5NGU0_A0A2K5NGU0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3M5V1_A0A2I3M5V1_PAPAN_9555 and tr_A0A2K6A326_A0A2K6A326_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091F1H9_A0A091F1H9_CORBR_85066 and tr_A0A093PTT4_A0A093PTT4_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091F1H9_A0A091F1H9_CORBR_85066 and tr_A0A218VBP3_A0A218VBP3_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0V1CWA8_A0A0V1CWA8_TRIBR_45882 and tr_A0A0V0V9H6_A0A0V0V9H6_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CWA8_A0A0V1CWA8_TRIBR_45882 and tr_A0A0V1LAK8_A0A0V1LAK8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CWA8_A0A0V1CWA8_TRIBR_45882 and tr_A0A0V0TWJ0_A0A0V0TWJ0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WVM5_A0A0V0WVM5_9BILA_92179 and tr_A0A0V1AFK8_A0A0V1AFK8_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A195BQ22_A0A195BQ22_9HYME_520822 and tr_A0A195ESS5_A0A195ESS5_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A2D0Q8M8_A0A2D0Q8M8_ICTPU_7998 and tr_A0A2D0QB94_A0A2D0QB94_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R2I7_A0A2D0R2I7_ICTPU_7998 and tr_A0A2D0R404_A0A2D0R404_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4B3T0_A0A2U4B3T0_TURTR_9739 and tr_A0A2U4B482_A0A2U4B482_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4B3U7_A0A2U4B3U7_TURTR_9739 and tr_A0A2U4B3Y6_A0A2U4B3Y6_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2Y9PMT5_A0A2Y9PMT5_DELLE_9749 and tr_A0A384B103_A0A384B103_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 44 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/4_raxmlng_ancestral/Q6ZUT3.raxml.reduced.phy Alignment comprises 1 partitions and 714 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 714 Gaps: 30.76 % Invariant sites: 0.98 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/4_raxmlng_ancestral/Q6ZUT3.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/3_mltree/Q6ZUT3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 179 / 14320 [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: -222321.051510 [00:00:00 -222321.051510] Initial branch length optimization [00:00:01 -185331.197328] Model parameter optimization (eps = 0.100000) [00:00:54] Tree #1, final logLikelihood: -184873.440577 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.147507,0.322344) (0.155264,0.418859) (0.295471,0.734885) (0.401759,1.668368) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/4_raxmlng_ancestral/Q6ZUT3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/4_raxmlng_ancestral/Q6ZUT3.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/4_raxmlng_ancestral/Q6ZUT3.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q6ZUT3/4_raxmlng_ancestral/Q6ZUT3.raxml.log Analysis started: 19-Jun-2021 20:51:01 / finished: 19-Jun-2021 20:52:01 Elapsed time: 60.793 seconds