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 14:09:43 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08426/2_msa/Q08426_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08426/3_mltree/Q08426.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08426/4_raxmlng_ancestral/Q08426 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804983 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/Q08426/2_msa/Q08426_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 723 sites WARNING: Sequences tr_B4Q7T9_B4Q7T9_DROSI_7240 and tr_B4HYZ1_B4HYZ1_DROSE_7238 are exactly identical! WARNING: Sequences tr_B2WEG8_B2WEG8_PYRTR_426418 and tr_A0A2W1I9Q8_A0A2W1I9Q8_9PLEO_45151 are exactly identical! WARNING: Sequences tr_Q29NA3_Q29NA3_DROPS_46245 and tr_B4G819_B4G819_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NYZ2_B8NYZ2_ASPFN_332952 and tr_Q2PIU9_Q2PIU9_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NYZ2_B8NYZ2_ASPFN_332952 and tr_A0A1S9D415_A0A1S9D415_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179V427_A0A179V427_BLAGS_559298 and tr_C5GWU1_C5GWU1_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A0E0FLC6_A0A0E0FLC6_ORYNI_4536 and tr_B8A7J7_B8A7J7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0FLC6_A0A0E0FLC6_ORYNI_4536 and tr_Q94CN1_Q94CN1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0FUE0_A0A0E0FUE0_ORYNI_4536 and tr_A2WVZ2_A2WVZ2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0FUE0_A0A0E0FUE0_ORYNI_4536 and tr_I1NSD7_I1NSD7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0FUE0_A0A0E0FUE0_ORYNI_4536 and tr_A0A0D3EV13_A0A0D3EV13_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0FUE0_A0A0E0FUE0_ORYNI_4536 and tr_A0A0D9YG29_A0A0D9YG29_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0FUE0_A0A0E0FUE0_ORYNI_4536 and tr_Q8S1G9_Q8S1G9_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2R2E2_A2R2E2_ASPNC_425011 and tr_A0A319BW03_A0A319BW03_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F4P0M5_F4P0M5_BATDJ_684364 and tr_A0A177WE61_A0A177WE61_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1NZC4_I1NZC4_ORYGL_4538 and tr_A0A0D3F3I0_A0A0D3F3I0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_E3MAW6_E3MAW6_CAERE_31234 and tr_A0A261CLY9_A0A261CLY9_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8XG18_A8XG18_CAEBR_6238 and tr_A0A2G5VKG7_A0A2G5VKG7_9PELO_1611254 are exactly identical! WARNING: Sequences tr_U5HFD7_U5HFD7_USTV1_683840 and tr_A0A2X0M5M2_A0A2X0M5M2_9BASI_796604 are exactly identical! WARNING: Sequences tr_A0A015LX37_A0A015LX37_9GLOM_1432141 and tr_A0A2H5TCT0_A0A2H5TCT0_RHIID_747089 are exactly identical! WARNING: Sequences tr_V4TV49_V4TV49_9ROSI_85681 and tr_A0A2H5QMF9_A0A2H5QMF9_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0E9N984_A0A0E9N984_SAICN_698492 and tr_A0A0E9NA54_A0A0E9NA54_SAICN_698492 are exactly identical! WARNING: Sequences tr_A0A0F8TX00_A0A0F8TX00_9EURO_308745 and tr_A0A2T5LVB7_A0A2T5LVB7_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0A1PAZ1_A0A0A1PAZ1_9FUNG_58291 and tr_A0A367J875_A0A367J875_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A100ILE8_A0A100ILE8_ASPNG_5061 and tr_A0A1L9NKU2_A0A1L9NKU2_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A146FGM3_A0A146FGM3_9EURO_1069201 and tr_A0A317VWL0_A0A317VWL0_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A1S4A6H4_A0A1S4A6H4_TOBAC_4097 and tr_A0A1U7VJ13_A0A1U7VJ13_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CRG7_A0A1S4CRG7_TOBAC_4097 and tr_A0A1U7YKG8_A0A1U7YKG8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2I1H5N7_A0A2I1H5N7_9GLOM_588596 and tr_A0A2H5UE82_A0A2H5UE82_RHIID_747089 are exactly identical! WARNING: Duplicate sequences found: 29 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/Q08426/4_raxmlng_ancestral/Q08426.raxml.reduced.phy Alignment comprises 1 partitions and 723 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 723 Gaps: 32.96 % Invariant sites: 0.55 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08426/4_raxmlng_ancestral/Q08426.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/Q08426/3_mltree/Q08426.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 181 / 14480 [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: -258618.831331 [00:00:00 -258618.831331] Initial branch length optimization [00:00:01 -258226.153184] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -257561.500292 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.156457,0.377467) (0.219864,0.442411) (0.353527,0.904831) (0.270153,1.938870) 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/Q08426/4_raxmlng_ancestral/Q08426.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08426/4_raxmlng_ancestral/Q08426.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08426/4_raxmlng_ancestral/Q08426.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08426/4_raxmlng_ancestral/Q08426.raxml.log Analysis started: 04-Jun-2021 14:09:43 / finished: 04-Jun-2021 14:10:31 Elapsed time: 47.934 seconds