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 17-Jul-2021 08:43:24 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96GA7/2_msa/Q96GA7_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96GA7/3_mltree/Q96GA7.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96GA7/4_raxmlng_ancestral/Q96GA7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626500604 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_300621/phylogeny-snakemake/results/Q96GA7/2_msa/Q96GA7_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 329 sites WARNING: Sequences tr_J3K6M7_J3K6M7_COCIM_246410 and tr_E9D1W4_E9D1W4_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3K6M7_J3K6M7_COCIM_246410 and tr_A0A0J7AYM5_A0A0J7AYM5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2WAH4_B2WAH4_PYRTR_426418 and tr_A0A2W1CVB9_A0A2W1CVB9_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8N9Q5_B8N9Q5_ASPFN_332952 and tr_Q2UGM2_Q2UGM2_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N9Q5_B8N9Q5_ASPFN_332952 and tr_A0A1S9DZ38_A0A1S9DZ38_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UDY0_A0A179UDY0_BLAGS_559298 and tr_C5GHI8_C5GHI8_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A179UE51_A0A179UE51_BLAGS_559298 and tr_C5GDJ4_C5GDJ4_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2Q6Y2_H2Q6Y2_PANTR_9598 and tr_A0A2R9BYD8_A0A2R9BYD8_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9G2V9_F9G2V9_FUSOF_660025 and tr_A0A0D2XB93_A0A0D2XB93_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9G2V9_F9G2V9_FUSOF_660025 and tr_X0CQN6_X0CQN6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G2V9_F9G2V9_FUSOF_660025 and tr_A0A2H3SR88_A0A2H3SR88_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9G2V9_F9G2V9_FUSOF_660025 and tr_A0A2H3I7U7_A0A2H3I7U7_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9G2V9_F9G2V9_FUSOF_660025 and tr_A0A365MV49_A0A365MV49_GIBIN_948311 are exactly identical! WARNING: Sequences tr_J5K740_J5K740_BEAB2_655819 and tr_A0A0A2VSE6_A0A0A2VSE6_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J5K740_J5K740_BEAB2_655819 and tr_A0A2N6NLM1_A0A2N6NLM1_BEABA_176275 are exactly identical! WARNING: Sequences tr_A2QI44_A2QI44_ASPNC_425011 and tr_G3Y8P2_G3Y8P2_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QI44_A2QI44_ASPNC_425011 and tr_A0A319B872_A0A319B872_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F6Z3Z0_F6Z3Z0_MACMU_9544 and tr_A0A0D9S482_A0A0D9S482_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6Z3Z0_F6Z3Z0_MACMU_9544 and tr_A0A2K5NHZ2_A0A2K5NHZ2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BEL5_F7BEL5_MACMU_9544 and tr_A0A2K6DCE5_A0A2K6DCE5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7X6U1_G7X6U1_ASPKW_1033177 and tr_A0A146FIN0_A0A146FIN0_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F9X1F6_F9X1F6_ZYMTI_336722 and tr_A0A1X7RGJ0_A0A1X7RGJ0_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2Y1G5_G2Y1G5_BOTF4_999810 and tr_M7U631_M7U631_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_G2YH95_G2YH95_BOTF4_999810 and tr_M7TJ42_M7TJ42_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_W7LLD6_W7LLD6_GIBM7_334819 and tr_A0A2K0WCM8_A0A2K0WCM8_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A0D2XCL5_A0A0D2XCL5_FUSO4_426428 and tr_X0D931_X0D931_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0D2XCL5_A0A0D2XCL5_FUSO4_426428 and tr_A0A2H3T4Z9_A0A2H3T4Z9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A0D2XCL5_A0A0D2XCL5_FUSO4_426428 and tr_A0A2H3HM24_A0A2H3HM24_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F2PW36_F2PW36_TRIEC_559882 and tr_A0A059J7B1_A0A059J7B1_9EURO_1215338 are exactly identical! WARNING: Sequences tr_W2PW42_W2PW42_PHYPN_761204 and tr_A0A0W8C7Y4_A0A0W8C7Y4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PW42_W2PW42_PHYPN_761204 and tr_W2KQF8_W2KQF8_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0B4IGZ5_A0A0B4IGZ5_METMF_1276143 and tr_A0A0D9P1F3_A0A0D9P1F3_METAN_1291518 are exactly identical! WARNING: Sequences tr_A0A0F0IM12_A0A0F0IM12_ASPPU_1403190 and tr_A0A2G7GAZ9_A0A2G7GAZ9_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F8XRP2_A0A0F8XRP2_9EURO_308745 and tr_A0A2T5LLC4_A0A2T5LLC4_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A100IA82_A0A100IA82_ASPNG_5061 and tr_A0A1L9MWJ1_A0A1L9MWJ1_ASPTU_767770 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_300621/phylogeny-snakemake/results/Q96GA7/4_raxmlng_ancestral/Q96GA7.raxml.reduced.phy Alignment comprises 1 partitions and 329 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 329 Gaps: 8.76 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96GA7/4_raxmlng_ancestral/Q96GA7.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_300621/phylogeny-snakemake/results/Q96GA7/3_mltree/Q96GA7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 83 / 6640 [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: -207445.781662 [00:00:00 -207445.781662] Initial branch length optimization [00:00:01 -207074.959619] Model parameter optimization (eps = 0.100000) [00:00:25] Tree #1, final logLikelihood: -206470.713598 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.170119,0.380208) (0.258896,0.424125) (0.292386,0.906922) (0.278599,2.011289) 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_300621/phylogeny-snakemake/results/Q96GA7/4_raxmlng_ancestral/Q96GA7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96GA7/4_raxmlng_ancestral/Q96GA7.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96GA7/4_raxmlng_ancestral/Q96GA7.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96GA7/4_raxmlng_ancestral/Q96GA7.raxml.log Analysis started: 17-Jul-2021 08:43:24 / finished: 17-Jul-2021 08:43:52 Elapsed time: 28.112 seconds