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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 12-Jul-2021 17:15:12 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/2_msa/Q16650_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/3_mltree/Q16650.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/4_raxmlng_ancestral/Q16650 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099312 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/2_msa/Q16650_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 682 sites WARNING: Sequences tr_A0A1D5P6N0_A0A1D5P6N0_CHICK_9031 and tr_A0A226NPL5_A0A226NPL5_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5P6N0_A0A1D5P6N0_CHICK_9031 and tr_A0A226PBE1_A0A226PBE1_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3XN95_M3XN95_MUSPF_9669 and tr_A0A337SM91_A0A337SM91_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XN95_M3XN95_MUSPF_9669 and tr_A0A2U3WMK7_A0A2U3WMK7_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XN95_M3XN95_MUSPF_9669 and tr_A0A2U3XX11_A0A2U3XX11_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1QNB4_G1QNB4_NOMLE_61853 and tr_G3I178_G3I178_CRIGR_10029 are exactly identical! WARNING: Sequences tr_G1QNB4_G1QNB4_NOMLE_61853 and tr_H0V6I7_H0V6I7_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G1QNB4_G1QNB4_NOMLE_61853 and tr_A0A2R8ZNR7_A0A2R8ZNR7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QXI2_G3QXI2_GORGO_9595 and tr_H2QU10_H2QU10_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QXI2_G3QXI2_GORGO_9595 and sp_O15178_TBXT_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QXI2_G3QXI2_GORGO_9595 and tr_A0A2R9A9Z3_A0A2R9A9Z3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RD44_G3RD44_GORGO_9595 and tr_A0A2J8XKH3_A0A2J8XKH3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RD44_G3RD44_GORGO_9595 and sp_Q99593_TBX5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RD44_G3RD44_GORGO_9595 and tr_F7I9Q2_F7I9Q2_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RD44_G3RD44_GORGO_9595 and tr_A0A2I3M7F5_A0A2I3M7F5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RD44_G3RD44_GORGO_9595 and tr_A0A0D9S4A3_A0A0D9S4A3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RD44_G3RD44_GORGO_9595 and tr_A0A2K5LIE8_A0A2K5LIE8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RD44_G3RD44_GORGO_9595 and tr_A0A2R9A5H2_A0A2R9A5H2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RS35_G3RS35_GORGO_9595 and tr_H2P7N0_H2P7N0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RS35_G3RS35_GORGO_9595 and tr_H2R3Y6_H2R3Y6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RS35_G3RS35_GORGO_9595 and sp_Q16650_TBR1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RS35_G3RS35_GORGO_9595 and tr_F6UNF8_F6UNF8_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RS35_G3RS35_GORGO_9595 and tr_A0A096MY32_A0A096MY32_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RS35_G3RS35_GORGO_9595 and tr_A0A0D9RT01_A0A0D9RT01_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RS35_G3RS35_GORGO_9595 and tr_A0A2K5LMC7_A0A2K5LMC7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RS35_G3RS35_GORGO_9595 and tr_A0A2K6BDW0_A0A2K6BDW0_MACNE_9545 are exactly identical! WARNING: Sequences tr_Q29F60_Q29F60_DROPS_46245 and tr_B4HB12_B4HB12_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RHN2_E2RHN2_CANLF_9615 and sp_Q861Q9_TBX4_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3RJU5_A0A2I3RJU5_PANTR_9598 and sp_O60806_TBX19_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RJU5_A0A2I3RJU5_PANTR_9598 and tr_A0A2R9AKY2_A0A2R9AKY2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QDA5_H2QDA5_PANTR_9598 and sp_Q9UL17_TBX21_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QDL3_H2QDL3_PANTR_9598 and sp_Q13207_TBX2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6YLI5_F6YLI5_MONDO_13616 and tr_G3WVW3_G3WVW3_SARHA_9305 are exactly identical! WARNING: Sequences tr_F7ARP2_F7ARP2_MACMU_9544 and tr_A0A2K5N1Q1_A0A2K5N1Q1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7ARP2_F7ARP2_MACMU_9544 and tr_A0A2K6DC73_A0A2K6DC73_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7ARP2_F7ARP2_MACMU_9544 and tr_A0A2K5XXF9_A0A2K5XXF9_MANLE_9568 are exactly identical! WARNING: Sequences tr_U3JPF3_U3JPF3_FICAL_59894 and tr_A0A218VAX7_A0A218VAX7_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A096NDV4_A0A096NDV4_PAPAN_9555 and tr_A0A2K5L7W9_A0A2K5L7W9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NDV4_A0A096NDV4_PAPAN_9555 and tr_A0A2K5Z7F2_A0A2K5Z7F2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NHQ7_A0A096NHQ7_PAPAN_9555 and tr_A0A2K5KIE3_A0A2K5KIE3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A093PUT9_A0A093PUT9_9PASS_328815 and tr_A0A091GAR1_A0A091GAR1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A093PUT9_A0A093PUT9_9PASS_328815 and tr_A0A0A0AN11_A0A0A0AN11_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093PUT9_A0A093PUT9_9PASS_328815 and tr_A0A091I0I4_A0A091I0I4_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1D342_A0A0V1D342_TRIBR_45882 and tr_A0A0V1NSI6_A0A0V1NSI6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D342_A0A0V1D342_TRIBR_45882 and tr_A0A0V0TYX1_A0A0V0TYX1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WIN9_A0A0V0WIN9_9BILA_92179 and tr_A0A0V1L6A2_A0A0V1L6A2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A226MNG5_A0A226MNG5_CALSU_9009 and tr_A0A226P9A9_A0A226P9A9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MZZ4_A0A226MZZ4_CALSU_9009 and tr_A0A226PAT9_A0A226PAT9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NBM1_A0A226NBM1_CALSU_9009 and tr_A0A226PG36_A0A226PG36_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5MRJ4_A0A2K5MRJ4_CERAT_9531 and tr_A0A2K5ZXI5_A0A2K5ZXI5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4AAP3_A0A2U4AAP3_TURTR_9739 and tr_A0A2Y9N8K5_A0A2Y9N8K5_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AAP3_A0A2U4AAP3_TURTR_9739 and tr_A0A2Y9SP41_A0A2Y9SP41_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 52 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/4_raxmlng_ancestral/Q16650.raxml.reduced.phy Alignment comprises 1 partitions and 682 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 682 Gaps: 43.42 % Invariant sites: 0.44 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/4_raxmlng_ancestral/Q16650.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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/3_mltree/Q16650.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 171 / 13680 [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: -230650.160286 [00:00:00 -230650.160286] Initial branch length optimization [00:00:02 -162751.383929] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -162369.526357 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.091493,0.117534) (0.124728,0.183693) (0.197498,0.608073) (0.586281,1.443407) 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/4_raxmlng_ancestral/Q16650.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/4_raxmlng_ancestral/Q16650.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/4_raxmlng_ancestral/Q16650.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q16650/4_raxmlng_ancestral/Q16650.raxml.log Analysis started: 12-Jul-2021 17:15:12 / finished: 12-Jul-2021 17:15:59 Elapsed time: 47.649 seconds Consumed energy: 2.268 Wh