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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 12-Jul-2021 18:24:28 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6UX41/2_msa/Q6UX41_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6UX41/3_mltree/Q6UX41.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6UX41/4_raxmlng_ancestral/Q6UX41 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626103468 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/Q6UX41/2_msa/Q6UX41_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 500 sites WARNING: Sequences sp_Q62158_TRI27_MOUSE_10090 and tr_A0A1U7R5Y1_A0A1U7R5Y1_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3XQ87_M3XQ87_MUSPF_9669 and tr_A0A2Y9IJR3_A0A2Y9IJR3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_F1P646_F1P646_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_G1M498_G1M498_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_M3VXS0_M3VXS0_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_A0A2U3ZPJ8_A0A2U3ZPJ8_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_A0A2U3XSM4_A0A2U3XSM4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_A0A2Y9JZW9_A0A2Y9JZW9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YK97_M3YK97_MUSPF_9669 and tr_A0A384C9P1_A0A384C9P1_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_G3RIJ4_G3RIJ4_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_K7EUW2_K7EUW2_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_H2QSK5_H2QSK5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and sp_P14373_TRI27_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_F7DCK3_F7DCK3_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A096NLL9_A0A096NLL9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A0D9R6T3_A0A0D9R6T3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A2K5N1H5_A0A2K5N1H5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A2K6B8E9_A0A2K6B8E9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A2K5YG76_A0A2K5YG76_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3HN16_A0A2I3HN16_NOMLE_61853 and tr_A0A2R9BGL3_A0A2R9BGL3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_G3RJV6_G3RJV6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_H2PIE3_H2PIE3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and sp_Q1XHU0_TRI39_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and sp_Q9HCM9_TRI39_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_F7BHH4_F7BHH4_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A2R8MSH2_A0A2R8MSH2_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A2I3NHT9_A0A2I3NHT9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A0D9R725_A0A0D9R725_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A1U7V4Q4_A0A1U7V4Q4_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A2K5P029_A0A2K5P029_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A2K5YXE4_A0A2K5YXE4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QYU1_G1QYU1_NOMLE_61853 and tr_A0A2R9C250_A0A2R9C250_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QWV0_G3QWV0_GORGO_9595 and tr_A0A2I3TLF3_A0A2I3TLF3_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2Q2Y1_H2Q2Y1_PANTR_9598 and sp_P19474_RO52_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q2Y1_H2Q2Y1_PANTR_9598 and tr_A0A2R9CHV1_A0A2R9CHV1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QSH7_H2QSH7_PANTR_9598 and tr_A0A2R9BIQ5_A0A2R9BIQ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_G3T9K8_G3T9K8_LOXAF_9785 are exactly identical! WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_K7GND2_K7GND2_PIG_9823 are exactly identical! WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_Q1LZA9_Q1LZA9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_A0A2U3VAG6_A0A2U3VAG6_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5Q7H3_W5Q7H3_SHEEP_9940 and tr_A0A2Y9M7Y8_A0A2Y9M7Y8_DELLE_9749 are exactly identical! WARNING: Sequences tr_G5C3B1_G5C3B1_HETGA_10181 and tr_A0A091D498_A0A091D498_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G1M9B4_G1M9B4_AILME_9646 and tr_A0A384DEQ3_A0A384DEQ3_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A0D9QW70_A0A0D9QW70_CHLSB_60711 and tr_A0A2K5LKX8_A0A2K5LKX8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9QW70_A0A0D9QW70_CHLSB_60711 and tr_A0A2K5YAG4_A0A2K5YAG4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091V6Y1_A0A091V6Y1_OPIHO_30419 and tr_A0A091GQX6_A0A091GQX6_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091V6Y1_A0A091V6Y1_OPIHO_30419 and tr_A0A0A0AK23_A0A0A0AK23_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2U3V9R2_A0A2U3V9R2_TURTR_9739 and tr_A0A2Y9MAZ9_A0A2Y9MAZ9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3WQ74_A0A2U3WQ74_ODORO_9708 and tr_A0A2U3Y010_A0A2U3Y010_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9MXG3_A0A2Y9MXG3_DELLE_9749 and tr_A0A2Y9EPM4_A0A2Y9EPM4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9MXG3_A0A2Y9MXG3_DELLE_9749 and tr_A0A384B2Y7_A0A384B2Y7_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 51 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/Q6UX41/4_raxmlng_ancestral/Q6UX41.raxml.reduced.phy Alignment comprises 1 partitions and 500 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 500 Gaps: 32.22 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6UX41/4_raxmlng_ancestral/Q6UX41.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/Q6UX41/3_mltree/Q6UX41.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 125 / 10000 [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: -243378.433386 [00:00:00 -243378.433386] Initial branch length optimization [00:00:03 -241802.790208] Model parameter optimization (eps = 0.100000) [00:00:53] Tree #1, final logLikelihood: -240520.639760 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.118702,0.608891) (0.102189,0.562142) (0.445682,0.892524) (0.333427,1.417092) 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/Q6UX41/4_raxmlng_ancestral/Q6UX41.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6UX41/4_raxmlng_ancestral/Q6UX41.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6UX41/4_raxmlng_ancestral/Q6UX41.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6UX41/4_raxmlng_ancestral/Q6UX41.raxml.log Analysis started: 12-Jul-2021 18:24:28 / finished: 12-Jul-2021 18:25:26 Elapsed time: 58.718 seconds Consumed energy: 4.401 Wh