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 14:15:34 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEZ3/2_msa/Q8NEZ3_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEZ3/3_mltree/Q8NEZ3.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEZ3/4_raxmlng_ancestral/Q8NEZ3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805334 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/Q8NEZ3/2_msa/Q8NEZ3_nogap_msa.fasta [00:00:00] Loaded alignment with 625 taxa and 1342 sites WARNING: Sequences tr_V7CZ60_V7CZ60_PHAVU_3885 and tr_A0A1S3TN82_A0A1S3TN82_VIGRR_3916 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_F6WPH9_F6WPH9_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_W5PSG6_W5PSG6_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_H0XAM8_H0XAM8_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_K7FYX4_K7FYX4_PELSI_13735 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_Q5H7B9_Q5H7B9_PIG_9823 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_Q32L05_Q32L05_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_A0A337SP30_A0A337SP30_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_U3KAN0_U3KAN0_FICAL_59894 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_U3IE02_U3IE02_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_A0A151NGP9_A0A151NGP9_ALLMI_8496 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_A0A2I0LI00_A0A2I0LI00_COLLI_8932 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_A0A1U7RWR2_A0A1U7RWR2_ALLSI_38654 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_A0A1V4JZE9_A0A1V4JZE9_PATFA_372326 are exactly identical! WARNING: Sequences sp_Q9R1K5_FZR1_MOUSE_10090 and tr_A0A218USD1_A0A218USD1_9PASE_299123 are exactly identical! WARNING: Sequences tr_H2MKK5_H2MKK5_ORYLA_8090 and tr_A0A1S3R4X6_A0A1S3R4X6_SALSA_8030 are exactly identical! WARNING: Sequences tr_G1P0C1_G1P0C1_MYOLU_59463 and tr_E2R4Z3_E2R4Z3_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1P0C1_G1P0C1_MYOLU_59463 and tr_A0A2U3VKT1_A0A2U3VKT1_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1P0C1_G1P0C1_MYOLU_59463 and tr_A0A2U3Y4Z1_A0A2U3Y4Z1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1P0C1_G1P0C1_MYOLU_59463 and tr_A0A2Y9LX90_A0A2Y9LX90_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1P0C1_G1P0C1_MYOLU_59463 and tr_A0A2Y9THX4_A0A2Y9THX4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3HSJ7_G3HSJ7_CRIGR_10029 and tr_A0A1U7QXS7_A0A1U7QXS7_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QIF6_G3QIF6_GORGO_9595 and tr_K7ANJ1_K7ANJ1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QIF6_G3QIF6_GORGO_9595 and tr_F7GTB6_F7GTB6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QIF6_G3QIF6_GORGO_9595 and tr_A0A0D9RFI9_A0A0D9RFI9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QIF6_G3QIF6_GORGO_9595 and tr_A0A1S3FNW1_A0A1S3FNW1_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G3QIF6_G3QIF6_GORGO_9595 and tr_A0A2K6BAT4_A0A2K6BAT4_MACNE_9545 are exactly identical! WARNING: Sequences tr_M4AY25_M4AY25_XIPMA_8083 and tr_G3PR65_G3PR65_GASAC_69293 are exactly identical! WARNING: Sequences tr_M4AY25_M4AY25_XIPMA_8083 and tr_A0A087YD86_A0A087YD86_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AY25_M4AY25_XIPMA_8083 and tr_A0A1S3LZV8_A0A1S3LZV8_SALSA_8030 are exactly identical! WARNING: Sequences tr_M4AY25_M4AY25_XIPMA_8083 and tr_A0A060XC37_A0A060XC37_ONCMY_8022 are exactly identical! WARNING: Sequences tr_M4AY25_M4AY25_XIPMA_8083 and tr_A0A2U9BKB1_A0A2U9BKB1_SCOMX_52904 are exactly identical! WARNING: Sequences tr_A0A3B5KPW6_A0A3B5KPW6_TAKRU_31033 and tr_H3DCY6_H3DCY6_TETNG_99883 are exactly identical! WARNING: Sequences tr_A0A286XCI2_A0A286XCI2_CAVPO_10141 and tr_A0A091DEE4_A0A091DEE4_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A0E0FZJ1_A0A0E0FZJ1_ORYNI_4536 and tr_A0A0E0N875_A0A0E0N875_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GG25_A0A0E0GG25_ORYNI_4536 and tr_I1P713_I1P713_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GG25_A0A0E0GG25_ORYNI_4536 and tr_A0A0E0CUF0_A0A0E0CUF0_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GG25_A0A0E0GG25_ORYNI_4536 and tr_A0A0E0NP02_A0A0E0NP02_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GG25_A0A0E0GG25_ORYNI_4536 and tr_Q10SH0_Q10SH0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1NVN8_I1NVN8_ORYGL_4538 and tr_Q5JM92_Q5JM92_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_M4CPT0_M4CPT0_BRARP_51351 and tr_A0A0D3B105_A0A0D3B105_BRAOL_109376 are exactly identical! WARNING: Sequences tr_M2SU93_M2SU93_COCSN_665912 and tr_M2UNV2_M2UNV2_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2SU93_M2SU93_COCSN_665912 and tr_W6YFD8_W6YFD8_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2SU93_M2SU93_COCSN_665912 and tr_W6ZI02_W6ZI02_COCMI_930090 are exactly identical! WARNING: Sequences tr_W2QS66_W2QS66_PHYPN_761204 and tr_A0A0W8DY01_A0A0W8DY01_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QS66_W2QS66_PHYPN_761204 and tr_W2FM39_W2FM39_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0D2GH84_A0A0D2GH84_9EURO_5601 and tr_A0A1C1D1T8_A0A1C1D1T8_9EURO_86049 are exactly identical! WARNING: Sequences tr_A0A1V8U8C5_A0A1V8U8C5_9PEZI_1974281 and tr_A0A1V8U9X5_A0A1V8U9X5_9PEZI_1974281 are exactly identical! WARNING: Duplicate sequences found: 48 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/Q8NEZ3/4_raxmlng_ancestral/Q8NEZ3.raxml.reduced.phy Alignment comprises 1 partitions and 1342 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1342 Gaps: 46.75 % Invariant sites: 0.07 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEZ3/4_raxmlng_ancestral/Q8NEZ3.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/Q8NEZ3/3_mltree/Q8NEZ3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 336 / 26880 [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: -279291.263462 [00:00:00 -279291.263462] Initial branch length optimization [00:00:01 -274946.540053] Model parameter optimization (eps = 0.100000) [00:00:50] Tree #1, final logLikelihood: -273595.386141 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.219242,0.424891) (0.194161,0.541004) (0.361410,0.990073) (0.225187,1.971615) 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/Q8NEZ3/4_raxmlng_ancestral/Q8NEZ3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEZ3/4_raxmlng_ancestral/Q8NEZ3.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEZ3/4_raxmlng_ancestral/Q8NEZ3.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q8NEZ3/4_raxmlng_ancestral/Q8NEZ3.raxml.log Analysis started: 04-Jun-2021 14:15:34 / finished: 04-Jun-2021 14:16:31 Elapsed time: 57.697 seconds