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 13:47:08 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P08237/2_msa/P08237_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P08237/3_mltree/P08237.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P08237/4_raxmlng_ancestral/P08237 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803628 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/P08237/2_msa/P08237_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 780 sites WARNING: Sequences tr_M3XMY8_M3XMY8_MUSPF_9669 and tr_A0A2Y9KQM1_A0A2Y9KQM1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_J3K6E3_J3K6E3_COCIM_246410 and tr_A0A0J7BAL1_A0A0J7BAL1_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QU79_B6QU79_TALMQ_441960 and tr_A0A093UWD4_A0A093UWD4_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3QUC7_G3QUC7_GORGO_9595 and tr_K7AUT0_K7AUT0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QUC7_G3QUC7_GORGO_9595 and sp_P08237_PFKAM_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QUC7_G3QUC7_GORGO_9595 and tr_A0A2R9BRB6_A0A2R9BRB6_PANPA_9597 are exactly identical! WARNING: Sequences tr_B8N0K5_B8N0K5_ASPFN_332952 and sp_Q9HGZ1_PFKA1_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N0K5_B8N0K5_ASPFN_332952 and tr_L7X1Q7_L7X1Q7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_K7DD35_K7DD35_PANTR_9598 and sp_P17858_PFKAL_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F9FL35_F9FL35_FUSOF_660025 and tr_N4UZ06_N4UZ06_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FL35_F9FL35_FUSOF_660025 and tr_X0CT46_X0CT46_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FL35_F9FL35_FUSOF_660025 and tr_A0A2H3HN93_A0A2H3HN93_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FL35_F9FL35_FUSOF_660025 and tr_A0A2K0WTN5_A0A2K0WTN5_GIBNY_42673 are exactly identical! WARNING: Sequences tr_C6H5H8_C6H5H8_AJECH_544712 and tr_F0UHI8_F0UHI8_AJEC8_544711 are exactly identical! WARNING: Sequences tr_J5JLS5_J5JLS5_BEAB2_655819 and tr_A0A0A2VDL5_A0A0A2VDL5_BEABA_1245745 are exactly identical! WARNING: Sequences tr_A0A0K0JQW2_A0A0K0JQW2_BRUMA_6279 and tr_A0A0R3R804_A0A0R3R804_9BILA_42155 are exactly identical! WARNING: Sequences tr_E2PSZ1_E2PSZ1_ASPNC_425011 and tr_G3YDJ6_G3YDJ6_ASPNA_380704 are exactly identical! WARNING: Sequences tr_E2PSZ1_E2PSZ1_ASPNC_425011 and tr_A0A319A792_A0A319A792_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X8R9_G7X8R9_ASPKW_1033177 and tr_A0A124BYQ2_A0A124BYQ2_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7X8R9_G7X8R9_ASPKW_1033177 and tr_A0A146F6D3_A0A146F6D3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7X8R9_G7X8R9_ASPKW_1033177 and tr_A0A1L9NLH5_A0A1L9NLH5_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7X8R9_G7X8R9_ASPKW_1033177 and tr_A0A317VII8_A0A317VII8_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A3Q0KF43_A0A3Q0KF43_SCHMA_6183 and tr_G4VKA6_G4VKA6_SCHMA_6183 are exactly identical! WARNING: Sequences tr_F2SSI3_F2SSI3_TRIRC_559305 and tr_A0A178EXZ3_A0A178EXZ3_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G7PHQ1_G7PHQ1_MACFA_9541 and tr_A0A096N5N7_A0A096N5N7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PHQ1_G7PHQ1_MACFA_9541 and tr_A0A0D9R1W6_A0A0D9R1W6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PHQ1_G7PHQ1_MACFA_9541 and tr_A0A2K5L904_A0A2K5L904_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PHQ1_G7PHQ1_MACFA_9541 and tr_A0A2K6CRU3_A0A2K6CRU3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PHQ1_G7PHQ1_MACFA_9541 and tr_A0A2K5XIR5_A0A2K5XIR5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F2PT69_F2PT69_TRIEC_559882 and tr_A0A059JEV4_A0A059JEV4_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L0PEQ8_L0PEQ8_PNEJ8_1209962 and tr_A0A0W4ZTZ4_A0A0W4ZTZ4_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_S0DSR8_S0DSR8_GIBF5_1279085 and tr_A0A2H3TQG4_A0A2H3TQG4_FUSOX_5507 are exactly identical! WARNING: Sequences tr_V2YAR9_V2YAR9_MONRO_1381753 and tr_A0A0W0F3F5_A0A0W0F3F5_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015IEQ5_A0A015IEQ5_9GLOM_1432141 and tr_U9TA57_U9TA57_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0F8UUK9_A0A0F8UUK9_9EURO_308745 and tr_A0A2T5LVV3_A0A2T5LVV3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0A1NGN9_A0A0A1NGN9_9FUNG_58291 and tr_A0A367JM72_A0A367JM72_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0V1CHX3_A0A0V1CHX3_TRIBR_45882 and tr_A0A0V0VA28_A0A0V0VA28_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CHX3_A0A0V1CHX3_TRIBR_45882 and tr_A0A0V0TP01_A0A0V0TP01_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1DE77_A0A0V1DE77_TRIBR_45882 and tr_A0A0V0U7D9_A0A0V0U7D9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1NFJ8_A0A0V1NFJ8_9BILA_92180 and tr_A0A0V0TV31_A0A0V0TV31_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A164TJC2_A0A164TJC2_9HOMO_1314777 and tr_A0A166E0Y4_A0A166E0Y4_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A226NHU8_A0A226NHU8_CALSU_9009 and tr_A0A226PAT3_A0A226PAT3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0S0D8_A0A2D0S0D8_ICTPU_7998 and tr_A0A2D0S214_A0A2D0S214_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S1Y5_A0A2D0S1Y5_ICTPU_7998 and tr_A0A2D0S204_A0A2D0S204_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 44 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/P08237/4_raxmlng_ancestral/P08237.raxml.reduced.phy Alignment comprises 1 partitions and 780 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 780 Gaps: 4.71 % Invariant sites: 1.03 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P08237/4_raxmlng_ancestral/P08237.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/P08237/3_mltree/P08237.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 195 / 15600 [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: -282943.984779 [00:00:00 -282943.984779] Initial branch length optimization [00:00:02 -282177.192727] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -280944.330284 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.261091,0.345405) (0.323744,0.448712) (0.243171,1.103535) (0.171994,2.884992) 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/P08237/4_raxmlng_ancestral/P08237.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P08237/4_raxmlng_ancestral/P08237.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P08237/4_raxmlng_ancestral/P08237.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P08237/4_raxmlng_ancestral/P08237.raxml.log Analysis started: 04-Jun-2021 13:47:08 / finished: 04-Jun-2021 13:47:56 Elapsed time: 48.553 seconds