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 13:58:24 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16595/2_msa/Q16595_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16595/3_mltree/Q16595.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16595/4_raxmlng_ancestral/Q16595 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804304 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/Q16595/2_msa/Q16595_nogap_msa.fasta [00:00:00] Loaded alignment with 906 taxa and 210 sites WARNING: Sequences tr_A0A0E1RYQ4_A0A0E1RYQ4_COCIM_246410 and tr_E9CW91_E9CW91_COCPS_443226 are exactly identical! WARNING: Sequences tr_A0A0E1RYQ4_A0A0E1RYQ4_COCIM_246410 and tr_A0A0J6Y158_A0A0J6Y158_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QQ51_B6QQ51_TALMQ_441960 and tr_A0A093XT66_A0A093XT66_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2W661_B2W661_PYRTR_426418 and tr_A0A2W1FEP1_A0A2W1FEP1_9PLEO_45151 are exactly identical! WARNING: Sequences tr_D8RVZ2_D8RVZ2_SELML_88036 and tr_D8SVL6_D8SVL6_SELML_88036 are exactly identical! WARNING: Sequences tr_B8N0X3_B8N0X3_ASPFN_332952 and tr_A0A0F0IF90_A0A0F0IF90_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8N0X3_B8N0X3_ASPFN_332952 and tr_A0A1S9DLC2_A0A1S9DLC2_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8N0X3_B8N0X3_ASPFN_332952 and tr_A0A2G7EM14_A0A2G7EM14_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179UDE2_A0A179UDE2_BLAGS_559298 and tr_C5GFQ1_C5GFQ1_AJEDR_559297 are exactly identical! WARNING: Sequences tr_K7ALT0_K7ALT0_PANTR_9598 and tr_A0A2R9BWG5_A0A2R9BWG5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9F519_F9F519_FUSOF_660025 and tr_N4UFA4_N4UFA4_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9F519_F9F519_FUSOF_660025 and tr_X0D1F0_X0D1F0_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9F519_F9F519_FUSOF_660025 and tr_A0A2H3T0R6_A0A2H3T0R6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_C6H2J5_C6H2J5_AJECH_544712 and tr_F0U5E6_F0U5E6_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0FU73_A0A0E0FU73_ORYNI_4536 and tr_Q5ZAV6_Q5ZAV6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QJ83_A2QJ83_ASPNC_425011 and tr_G3Y9I6_G3Y9I6_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QJ83_A2QJ83_ASPNC_425011 and tr_A0A319BQP6_A0A319BQP6_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X882_G7X882_ASPKW_1033177 and tr_A0A146FJD8_A0A146FJD8_9EURO_1069201 are exactly identical! WARNING: Sequences tr_I1NS86_I1NS86_ORYGL_4538 and tr_A0A0D3EUU1_A0A0D3EUU1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G2YD21_G2YD21_BOTF4_999810 and tr_M7UJE1_M7UJE1_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A8WU33_A8WU33_CAEBR_6238 and tr_A0A2G5V490_A0A2G5V490_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SX59_F2SX59_TRIRC_559305 and tr_A0A178F7N9_A0A178F7N9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_W7M675_W7M675_GIBM7_334819 and tr_A0A2K0VTK0_A0A2K0VTK0_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A0D2XUQ7_A0A0D2XUQ7_FUSO4_426428 and tr_A0A2H3HS52_A0A2H3HS52_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F2PSV8_F2PSV8_TRIEC_559882 and tr_A0A059JH07_A0A059JH07_9EURO_1215338 are exactly identical! WARNING: Sequences tr_U5H797_U5H797_USTV1_683840 and tr_A0A2X0P6I8_A0A2X0P6I8_9BASI_796604 are exactly identical! WARNING: Sequences tr_W2R7Q3_W2R7Q3_PHYPN_761204 and tr_A0A0W8D0D7_A0A0W8D0D7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R7Q3_W2R7Q3_PHYPN_761204 and tr_W2NBF6_W2NBF6_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015L893_A0A015L893_9GLOM_1432141 and tr_A0A2I1GJW5_A0A2I1GJW5_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A094EER8_A0A094EER8_9PEZI_1420912 and tr_A0A1B8G8V8_A0A1B8G8V8_9PEZI_342668 are exactly identical! WARNING: Sequences tr_V4UEI0_V4UEI0_9ROSI_85681 and tr_A0A2H5PHY1_A0A2H5PHY1_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0A1MRS3_A0A0A1MRS3_9FUNG_58291 and tr_A0A367KE84_A0A367KE84_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1NXG2_A0A0A1NXG2_9FUNG_58291 and tr_A0A367JHF4_A0A367JHF4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0G4KN61_A0A0G4KN61_9PEZI_100787 and tr_A0A0G4L3N3_A0A0G4L3N3_9PEZI_100787 are exactly identical! WARNING: Sequences tr_A0A0G4PRK6_A0A0G4PRK6_PENCA_1429867 and tr_A0A101ML36_A0A101ML36_9EURO_48697 are exactly identical! WARNING: Sequences tr_A0A0G4PRK6_A0A0G4PRK6_PENCA_1429867 and tr_A0A1V6RD35_A0A1V6RD35_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0V1LGR6_A0A0V1LGR6_9BILA_6335 and tr_A0A0V1NJS4_A0A0V1NJS4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3M6J9_A0A1S3M6J9_SALSA_8030 and tr_A0A1S3M798_A0A1S3M798_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A3Q0EQN7_A0A3Q0EQN7_VIGRR_3916 and tr_A0A3Q0ET10_A0A3Q0ET10_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A1Q3EQ22_A0A1Q3EQ22_LENED_5353 and tr_A0A1Q3EQ50_A0A1Q3EQ50_LENED_5353 are exactly identical! WARNING: Sequences tr_A0A1Q3EQ22_A0A1Q3EQ22_LENED_5353 and tr_A0A1Q3EQD0_A0A1Q3EQD0_LENED_5353 are exactly identical! WARNING: Sequences tr_A0A2G2Z3B1_A0A2G2Z3B1_CAPAN_4072 and tr_A0A2G3C0H3_A0A2G3C0H3_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 42 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/Q16595/4_raxmlng_ancestral/Q16595.raxml.reduced.phy Alignment comprises 1 partitions and 210 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 210 Gaps: 33.82 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16595/4_raxmlng_ancestral/Q16595.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/Q16595/3_mltree/Q16595.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 53 / 4240 [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: -116078.218850 [00:00:00 -116078.218850] Initial branch length optimization [00:00:00 -105966.196402] Model parameter optimization (eps = 0.100000) [00:00:24] Tree #1, final logLikelihood: -105822.969594 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.108934,0.102296) (0.135624,0.204469) (0.242905,0.682890) (0.512537,1.551592) 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/Q16595/4_raxmlng_ancestral/Q16595.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16595/4_raxmlng_ancestral/Q16595.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16595/4_raxmlng_ancestral/Q16595.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16595/4_raxmlng_ancestral/Q16595.raxml.log Analysis started: 04-Jun-2021 13:58:24 / finished: 04-Jun-2021 13:58:50 Elapsed time: 25.778 seconds