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 14:12:50 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54840/2_msa/P54840_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54840/3_mltree/P54840.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54840/4_raxmlng_ancestral/P54840 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805170 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/P54840/2_msa/P54840_nogap_msa.fasta [00:00:00] Loaded alignment with 978 taxa and 703 sites WARNING: Sequences tr_B4QZ52_B4QZ52_DROSI_7240 and sp_Q9VFC8_GYS_DROME_7227 are exactly identical! WARNING: Sequences tr_M3XM89_M3XM89_MUSPF_9669 and tr_A0A2Y9L431_A0A2Y9L431_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A0D8JUE8_A0A0D8JUE8_COCIM_246410 and tr_A0A0J6Y4I3_A0A0J6Y4I3_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2WLZ8_B2WLZ8_PYRTR_426418 and tr_A0A2W1E704_A0A2W1E704_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3QU91_G3QU91_GORGO_9595 and tr_H2Q5L0_H2Q5L0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QU91_G3QU91_GORGO_9595 and tr_A0A2R9CAG3_A0A2R9CAG3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2WUB6_G2WUB6_VERDV_498257 and tr_C9SG41_C9SG41_VERA1_526221 are exactly identical! WARNING: Sequences tr_C0NTA6_C0NTA6_AJECG_447093 and tr_F0UP57_F0UP57_AJEC8_544711 are exactly identical! WARNING: Sequences sp_O93869_GYS_NEUCR_367110 and tr_G4UH34_G4UH34_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8NQ75_B8NQ75_ASPFN_332952 and tr_Q2UAJ3_Q2UAJ3_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NQ75_B8NQ75_ASPFN_332952 and tr_A0A1S9DS23_A0A1S9DS23_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UB39_A0A179UB39_BLAGS_559298 and tr_C5GIE4_C5GIE4_AJEDR_559297 are exactly identical! WARNING: Sequences tr_K7DM65_K7DM65_PANTR_9598 and sp_P13807_GYS1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7DM65_K7DM65_PANTR_9598 and tr_A0A2R9BUZ0_A0A2R9BUZ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FTD0_F9FTD0_FUSOF_660025 and tr_A0A0D2XDM3_A0A0D2XDM3_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FTD0_F9FTD0_FUSOF_660025 and tr_N4TZ75_N4TZ75_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FTD0_F9FTD0_FUSOF_660025 and tr_X0D238_X0D238_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FTD0_F9FTD0_FUSOF_660025 and tr_A0A2H3TNH2_A0A2H3TNH2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FTD0_F9FTD0_FUSOF_660025 and tr_A0A2H3HJN0_A0A2H3HJN0_FUSOX_327505 are exactly identical! WARNING: Sequences tr_J5JV80_J5JV80_BEAB2_655819 and tr_A0A0A2V9Y7_A0A0A2V9Y7_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J5JV80_J5JV80_BEAB2_655819 and tr_A0A2N6NKH4_A0A2N6NKH4_BEABA_176275 are exactly identical! WARNING: Sequences tr_A5AAD7_A5AAD7_ASPNC_425011 and tr_G3Y1A8_G3Y1A8_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A5AAD7_A5AAD7_ASPNC_425011 and tr_A0A319AI45_A0A319AI45_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F6ZV30_F6ZV30_MACMU_9544 and tr_A0A0A0MUR2_A0A0A0MUR2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7XBA8_G7XBA8_ASPKW_1033177 and tr_A0A146FDU9_A0A146FDU9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_E6R509_E6R509_CRYGW_367775 and tr_A0A095C3M6_A0A095C3M6_CRYGR_294750 are exactly identical! WARNING: Sequences tr_F9XHH4_F9XHH4_ZYMTI_336722 and tr_A0A1X7S183_A0A1X7S183_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2Y3W1_G2Y3W1_BOTF4_999810 and tr_M7U3L2_M7U3L2_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_W7MGK2_W7MGK2_GIBM7_334819 and tr_S0DU24_S0DU24_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_W7MGK2_W7MGK2_GIBM7_334819 and tr_A0A2K0VX49_A0A2K0VX49_GIBNY_42673 are exactly identical! WARNING: Sequences tr_V2X4W4_V2X4W4_MONRO_1381753 and tr_A0A0W0GFA0_A0A0W0GFA0_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015M151_A0A015M151_9GLOM_1432141 and tr_U9SK73_U9SK73_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096N5V0_A0A096N5V0_PAPAN_9555 and tr_A0A2K5YS85_A0A2K5YS85_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A094EIF8_A0A094EIF8_9PEZI_1420912 and tr_A0A1B8GL01_A0A1B8GL01_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0V1A941_A0A0V1A941_9BILA_990121 and tr_A0A0V1PEZ8_A0A0V1PEZ8_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1MYK2_A0A0V1MYK2_9BILA_268474 and tr_A0A0V1HYM9_A0A0V1HYM9_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A100IAB1_A0A100IAB1_ASPNG_5061 and tr_A0A1L9N8W1_A0A1L9N8W1_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A164WP25_A0A164WP25_9HOMO_1314777 and tr_A0A166DKS4_A0A166DKS4_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1B8AC58_A0A1B8AC58_FUSPO_36050 and tr_A0A2L2SZ79_A0A2L2SZ79_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A1V8TRC6_A0A1V8TRC6_9PEZI_1507870 and tr_A0A1V8TVD9_A0A1V8TVD9_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2H3CJP7_A0A2H3CJP7_ARMGA_47427 and tr_A0A2H3AYT4_A0A2H3AYT4_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A319D7M7_A0A319D7M7_9EURO_1448315 and tr_A0A2V5IKR7_A0A2V5IKR7_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A319D7M7_A0A319D7M7_9EURO_1448315 and tr_A0A2V5GQH1_A0A2V5GQH1_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 43 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/P54840/4_raxmlng_ancestral/P54840.raxml.reduced.phy Alignment comprises 1 partitions and 703 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 703 Gaps: 14.58 % Invariant sites: 0.14 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54840/4_raxmlng_ancestral/P54840.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/P54840/3_mltree/P54840.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 176 / 14080 [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: -176951.161105 [00:00:00 -176951.161105] Initial branch length optimization [00:00:01 -174769.540669] Model parameter optimization (eps = 0.100000) [00:00:50] Tree #1, final logLikelihood: -174237.249701 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.256235,0.337396) (0.328888,0.518284) (0.210213,0.960308) (0.204663,2.644447) 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/P54840/4_raxmlng_ancestral/P54840.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54840/4_raxmlng_ancestral/P54840.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54840/4_raxmlng_ancestral/P54840.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54840/4_raxmlng_ancestral/P54840.raxml.log Analysis started: 04-Jun-2021 14:12:50 / finished: 04-Jun-2021 14:13:46 Elapsed time: 56.266 seconds