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 04-Jun-2021 13:59:32 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6IQ55/2_msa/Q6IQ55_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6IQ55/3_mltree/Q6IQ55.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6IQ55/4_raxmlng_ancestral/Q6IQ55 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804372 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_020621/phylogeny-snakemake/results/Q6IQ55/2_msa/Q6IQ55_nogap_msa.fasta [00:00:00] Loaded alignment with 998 taxa and 1244 sites WARNING: Sequences tr_Q20018_Q20018_CAEEL_6239 and tr_Q21521_Q21521_CAEEL_6239 are exactly identical! WARNING: Sequences tr_A0A0H5S9X7_A0A0H5S9X7_BRUMA_6279 and tr_A0A0N4TM84_A0A0N4TM84_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0H5S9X7_A0A0H5S9X7_BRUMA_6279 and tr_A0A0R3QSH0_A0A0R3QSH0_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A0H5SKI9_A0A0H5SKI9_BRUMA_6279 and tr_A0A0R3R205_A0A0R3R205_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A0J9Y7S4_A0A0J9Y7S4_BRUMA_6279 and tr_A0A0N4TP96_A0A0N4TP96_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0K0JLZ4_A0A0K0JLZ4_BRUMA_6279 and tr_A0A0N4TNW2_A0A0N4TNW2_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A158PYM7_A0A158PYM7_BRUMA_6279 and tr_A0A0N4TUU5_A0A0N4TUU5_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A1P6C2K7_A0A1P6C2K7_BRUMA_6279 and tr_A0A0N4T0D4_A0A0N4T0D4_BRUPA_6280 are exactly identical! WARNING: Sequences tr_G0MZ25_G0MZ25_CAEBE_135651 and tr_G0MZ53_G0MZ53_CAEBE_135651 are exactly identical! WARNING: Sequences tr_G0NL57_G0NL57_CAEBE_135651 and tr_G0NQH0_G0NQH0_CAEBE_135651 are exactly identical! WARNING: Sequences tr_G0NLF7_G0NLF7_CAEBE_135651 and tr_G0NPZ8_G0NPZ8_CAEBE_135651 are exactly identical! WARNING: Sequences tr_E3LV27_E3LV27_CAERE_31234 and tr_A0A261C7F5_A0A261C7F5_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3LYQ9_E3LYQ9_CAERE_31234 and tr_A0A261AGN9_A0A261AGN9_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3MG46_E3MG46_CAERE_31234 and tr_A0A261AT90_A0A261AT90_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3MG67_E3MG67_CAERE_31234 and tr_A0A261AT70_A0A261AT70_9PELO_1503980 are exactly identical! WARNING: Sequences tr_W2Q1G0_W2Q1G0_PHYPN_761204 and tr_A0A0W8AYA5_A0A0W8AYA5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A044U4F7_A0A044U4F7_ONCVO_6282 and tr_A0A182E9A3_A0A182E9A3_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A044ULU4_A0A044ULU4_ONCVO_6282 and tr_A0A182EGJ4_A0A182EGJ4_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A044UP51_A0A044UP51_ONCVO_6282 and tr_A0A182EDF3_A0A182EDF3_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0K0F963_A0A0K0F963_STRVS_75913 and tr_A0A0N5C8G8_A0A0N5C8G8_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0V1CJS4_A0A0V1CJS4_TRIBR_45882 and tr_A0A0V0TC77_A0A0V0TC77_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D3V6_A0A0V1D3V6_TRIBR_45882 and tr_A0A0V0VW99_A0A0V0VW99_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D3V6_A0A0V1D3V6_TRIBR_45882 and tr_A0A0V0T6R1_A0A0V0T6R1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D5D7_A0A0V1D5D7_TRIBR_45882 and tr_A0A0V0VW25_A0A0V0VW25_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DE01_A0A0V1DE01_TRIBR_45882 and tr_A0A0V0VZY4_A0A0V0VZY4_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DE01_A0A0V1DE01_TRIBR_45882 and tr_A0A0V1LKG0_A0A0V1LKG0_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DE01_A0A0V1DE01_TRIBR_45882 and tr_A0A0V1PFQ2_A0A0V1PFQ2_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DE01_A0A0V1DE01_TRIBR_45882 and tr_A0A0V0U6X8_A0A0V0U6X8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WTJ0_A0A0V0WTJ0_9BILA_92179 and tr_A0A0V1LT55_A0A0V1LT55_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0UJ85_A0A0V0UJ85_9BILA_181606 and tr_A0A0V0UKI1_A0A0V0UKI1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1KN91_A0A0V1KN91_9BILA_6335 and tr_A0A0V1NK62_A0A0V1NK62_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1KN91_A0A0V1KN91_9BILA_6335 and tr_A0A0V0T200_A0A0V0T200_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1KUC2_A0A0V1KUC2_9BILA_6335 and tr_A0A0V0ZEI3_A0A0V0ZEI3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1LF85_A0A0V1LF85_9BILA_6335 and tr_A0A0V1PI35_A0A0V1PI35_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A2K5N0A6_A0A2K5N0A6_CERAT_9531 and tr_A0A2K6A7W1_A0A2K6A7W1_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 35 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6IQ55/4_raxmlng_ancestral/Q6IQ55.raxml.reduced.phy Alignment comprises 1 partitions and 1244 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1244 Gaps: 60.51 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6IQ55/4_raxmlng_ancestral/Q6IQ55.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_020621/phylogeny-snakemake/results/Q6IQ55/3_mltree/Q6IQ55.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 311 / 24880 [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: -358185.831189 [00:00:00 -358185.831189] Initial branch length optimization [00:00:03 -309781.018360] Model parameter optimization (eps = 0.100000) [00:02:09] Tree #1, final logLikelihood: -308749.552290 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.060156,0.173952) (0.079474,0.193695) (0.258809,0.570636) (0.601561,1.373853) 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_020621/phylogeny-snakemake/results/Q6IQ55/4_raxmlng_ancestral/Q6IQ55.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6IQ55/4_raxmlng_ancestral/Q6IQ55.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6IQ55/4_raxmlng_ancestral/Q6IQ55.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q6IQ55/4_raxmlng_ancestral/Q6IQ55.raxml.log Analysis started: 04-Jun-2021 13:59:32 / finished: 04-Jun-2021 14:01:52 Elapsed time: 139.935 seconds