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 14:20:06 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00311/2_msa/O00311_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00311/3_mltree/O00311.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00311/4_raxmlng_ancestral/O00311 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805606 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/O00311/2_msa/O00311_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 574 sites WARNING: Sequences tr_B4Q8F9_B4Q8F9_DROSI_7240 and tr_B4I5G2_B4I5G2_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3KKM0_J3KKM0_COCIM_246410 and tr_A0A0J6Y509_A0A0J6Y509_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QTI8_B6QTI8_TALMQ_441960 and tr_A0A093X9H7_A0A093X9H7_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WNW1_B2WNW1_PYRTR_426418 and tr_A0A2W1I3X0_A0A2W1I3X0_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8PJ81_B8PJ81_POSPM_561896 and tr_A0A1X6MTF0_A0A1X6MTF0_9APHY_670580 are exactly identical! WARNING: Sequences tr_B8NV89_B8NV89_ASPFN_332952 and tr_Q2U592_Q2U592_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NV89_B8NV89_ASPFN_332952 and tr_A0A1S9DII1_A0A1S9DII1_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179V1G4_A0A179V1G4_BLAGS_559298 and tr_C5GM83_C5GM83_AJEDR_559297 are exactly identical! WARNING: Sequences tr_C6H8Z8_C6H8Z8_AJECH_544712 and tr_F0UAD7_F0UAD7_AJEC8_544711 are exactly identical! WARNING: Sequences tr_J4WMW6_J4WMW6_BEAB2_655819 and tr_A0A2N6N9Z4_A0A2N6N9Z4_BEABA_176275 are exactly identical! WARNING: Sequences tr_A2QY28_A2QY28_ASPNC_425011 and tr_A0A319A341_A0A319A341_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A2R082_A2R082_ASPNC_425011 and tr_G3XW72_G3XW72_ASPNA_380704 are exactly identical! WARNING: Sequences tr_G7XL51_G7XL51_ASPKW_1033177 and tr_A0A146EXS0_A0A146EXS0_9EURO_1069201 are exactly identical! WARNING: Sequences tr_I1P3E1_I1P3E1_ORYGL_4538 and tr_A0A0E0NJP9_A0A0E0NJP9_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1P3E1_I1P3E1_ORYGL_4538 and sp_Q6Z8C8_CDKF4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G2YB80_G2YB80_BOTF4_999810 and tr_M7TH84_M7TH84_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SII9_F2SII9_TRIRC_559305 and tr_A0A178F1Q6_A0A178F1Q6_TRIRU_5551 are exactly identical! WARNING: Sequences tr_B3RP02_B3RP02_TRIAD_10228 and tr_A0A369SA66_A0A369SA66_9METZ_287889 are exactly identical! WARNING: Sequences tr_C4V6N2_C4V6N2_NOSCE_578460 and tr_A0A0F9WDY3_A0A0F9WDY3_9MICR_40302 are exactly identical! WARNING: Sequences tr_W7MHA7_W7MHA7_GIBM7_334819 and tr_A0A2K0W7E6_A0A2K0W7E6_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A0D2XJG3_A0A0D2XJG3_FUSO4_426428 and tr_X0CLX6_X0CLX6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_N4U6K0_N4U6K0_FUSC1_1229664 and tr_A0A2H3T9K8_A0A2H3T9K8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_M2TBP0_M2TBP0_COCSN_665912 and tr_M2UN24_M2UN24_COCH5_701091 are exactly identical! WARNING: Sequences tr_V2XPB3_V2XPB3_MONRO_1381753 and tr_A0A0W0G4K4_A0A0W0G4K4_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A0F0ILQ3_A0A0F0ILQ3_ASPPU_1403190 and tr_A0A2G7FZK9_A0A2G7FZK9_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F9XN67_A0A0F9XN67_TRIHA_5544 and tr_A0A2T3ZUD8_A0A2T3ZUD8_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0F8UXZ1_A0A0F8UXZ1_9EURO_308745 and tr_A0A2T5LKY6_A0A2T5LKY6_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V1CS98_A0A0V1CS98_TRIBR_45882 and tr_A0A0V1P0U6_A0A0V1P0U6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CS98_A0A0V1CS98_TRIBR_45882 and tr_A0A0V0UAU6_A0A0V0UAU6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A166N6J2_A0A166N6J2_9PEZI_708197 and tr_A0A167B071_A0A167B071_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_A0A1L9N2C4_A0A1L9N2C4_ASPTU_767770 and tr_A0A317UVT2_A0A317UVT2_9EURO_1448314 are exactly identical! WARNING: Duplicate sequences found: 31 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/O00311/4_raxmlng_ancestral/O00311.raxml.reduced.phy Alignment comprises 1 partitions and 574 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 574 Gaps: 36.31 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00311/4_raxmlng_ancestral/O00311.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/O00311/3_mltree/O00311.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 144 / 11520 [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: -254143.405172 [00:00:00 -254143.405172] Initial branch length optimization [00:00:01 -252699.063844] Model parameter optimization (eps = 0.100000) [00:00:53] Tree #1, final logLikelihood: -251819.657259 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.115543,0.231769) (0.142183,0.245561) (0.216602,0.564254) (0.525672,1.552466) 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/O00311/4_raxmlng_ancestral/O00311.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00311/4_raxmlng_ancestral/O00311.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00311/4_raxmlng_ancestral/O00311.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00311/4_raxmlng_ancestral/O00311.raxml.log Analysis started: 04-Jun-2021 14:20:06 / finished: 04-Jun-2021 14:21:04 Elapsed time: 58.310 seconds