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 02-Jun-2021 15:36:13 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y6A1/2_msa/Q9Y6A1_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y6A1/3_mltree/Q9Y6A1.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y6A1/4_raxmlng_ancestral/Q9Y6A1 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622637373 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/Q9Y6A1/2_msa/Q9Y6A1_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 747 sites WARNING: Sequences tr_J3KKV5_J3KKV5_COCIM_246410 and tr_A0A0J6YRZ0_A0A0J6YRZ0_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QTD7_B6QTD7_TALMQ_441960 and tr_A0A093VBH8_A0A093VBH8_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WAJ6_B2WAJ6_PYRTR_426418 and tr_A0A2W1HQS0_A0A2W1HQS0_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8N5D6_B8N5D6_ASPFN_332952 and tr_Q2UBF4_Q2UBF4_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N8F2_B8N8F2_ASPFN_332952 and tr_A0A1S9DY00_A0A1S9DY00_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NV10_B8NV10_ASPFN_332952 and tr_A0A1S9DIC0_A0A1S9DIC0_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UJM1_A0A179UJM1_BLAGS_559298 and tr_C5GUX9_C5GUX9_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A179US37_A0A179US37_BLAGS_559298 and tr_C5GPP0_C5GPP0_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FQ44_F9FQ44_FUSOF_660025 and tr_A0A0D2X980_A0A0D2X980_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FQ44_F9FQ44_FUSOF_660025 and tr_N4TEN9_N4TEN9_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FQ44_F9FQ44_FUSOF_660025 and tr_X0D067_X0D067_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FQ44_F9FQ44_FUSOF_660025 and tr_A0A2H3T1Z8_A0A2H3T1Z8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FQ44_F9FQ44_FUSOF_660025 and tr_A0A2H3HUW1_A0A2H3HUW1_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FQ44_F9FQ44_FUSOF_660025 and tr_A0A2K0W5T8_A0A2K0W5T8_GIBNY_42673 are exactly identical! WARNING: Sequences tr_C6HL67_C6HL67_AJECH_544712 and tr_F0UEA7_F0UEA7_AJEC8_544711 are exactly identical! WARNING: Sequences tr_C6HLV2_C6HLV2_AJECH_544712 and tr_F0UPW3_F0UPW3_AJEC8_544711 are exactly identical! WARNING: Sequences tr_G7XR29_G7XR29_ASPKW_1033177 and tr_A0A146FU20_A0A146FU20_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F9WYG9_F9WYG9_ZYMTI_336722 and tr_A0A1X7RGT2_A0A1X7RGT2_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F9XQ12_F9XQ12_ZYMTI_336722 and tr_A0A1X7S8Y5_A0A1X7S8Y5_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YTK5_G2YTK5_BOTF4_999810 and tr_M7TJS3_M7TJS3_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2STZ8_F2STZ8_TRIRC_559305 and tr_A0A178F7B9_A0A178F7B9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G3Y6U0_G3Y6U0_ASPNA_380704 and tr_A0A319BWV6_A0A319BWV6_9EURO_1450533 are exactly identical! WARNING: Sequences tr_L0P8U1_L0P8U1_PNEJ8_1209962 and tr_A0A0W4ZEP2_A0A0W4ZEP2_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_S0DP21_S0DP21_GIBF5_1279085 and tr_A0A365N682_A0A365N682_GIBIN_948311 are exactly identical! WARNING: Sequences tr_V2YXQ4_V2YXQ4_MONRO_1381753 and tr_A0A0W0FZ62_A0A0W0FZ62_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015IZF0_A0A015IZF0_9GLOM_1432141 and tr_U9TZC8_U9TZC8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015JYS1_A0A015JYS1_9GLOM_1432141 and tr_A0A2H5R6B4_A0A2H5R6B4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015M547_A0A015M547_9GLOM_1432141 and tr_U9TCS2_U9TCS2_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094EV96_A0A094EV96_9PEZI_1420912 and tr_A0A1B8GQQ7_A0A1B8GQQ7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F8U9L6_A0A0F8U9L6_9EURO_308745 and tr_A0A2T5M5M7_A0A2T5M5M7_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0A1MIL8_A0A0A1MIL8_9FUNG_58291 and tr_A0A367KGP2_A0A367KGP2_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A100ILR1_A0A100ILR1_ASPNG_5061 and tr_A0A1L9N4F7_A0A1L9N4F7_ASPTU_767770 are exactly identical! WARNING: Sequences tr_I1RAS3_I1RAS3_GIBZE_229533 and tr_A0A2T4H728_A0A2T4H728_FUSCU_5516 are exactly identical! WARNING: Duplicate sequences found: 33 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/Q9Y6A1/4_raxmlng_ancestral/Q9Y6A1.raxml.reduced.phy Alignment comprises 1 partitions and 747 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 747 Gaps: 11.79 % Invariant sites: 1.20 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y6A1/4_raxmlng_ancestral/Q9Y6A1.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/Q9Y6A1/3_mltree/Q9Y6A1.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 187 / 14960 [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: -316066.237994 [00:00:00 -316066.237994] Initial branch length optimization [00:00:01 -315309.663992] Model parameter optimization (eps = 0.100000) [00:00:37] Tree #1, final logLikelihood: -313799.821763 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.246387,0.402377) (0.300996,0.575753) (0.357553,1.382598) (0.095064,2.453163) 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/Q9Y6A1/4_raxmlng_ancestral/Q9Y6A1.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y6A1/4_raxmlng_ancestral/Q9Y6A1.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y6A1/4_raxmlng_ancestral/Q9Y6A1.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y6A1/4_raxmlng_ancestral/Q9Y6A1.raxml.log Analysis started: 02-Jun-2021 15:36:13 / finished: 02-Jun-2021 15:36:56 Elapsed time: 43.810 seconds