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 20-Jul-2021 16:35:11 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P98077/2_msa/P98077_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P98077/3_mltree/P98077.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P98077/4_raxmlng_ancestral/P98077 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626788111 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_300621/phylogeny-snakemake/results/P98077/2_msa/P98077_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 582 sites WARNING: Sequences tr_B4Q624_B4Q624_DROSI_7240 and tr_B4ICV4_B4ICV4_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QN62_B4QN62_DROSI_7240 and tr_Q9V3C8_Q9V3C8_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QN62_B4QN62_DROSI_7240 and tr_B4HKQ4_B4HKQ4_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QVG0_B4QVG0_DROSI_7240 and tr_B4ICF2_B4ICF2_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1RKA0_G1RKA0_NOMLE_61853 and tr_G3R3G4_G3R3G4_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RKA0_G1RKA0_NOMLE_61853 and tr_K7CY17_K7CY17_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RKA0_G1RKA0_NOMLE_61853 and sp_P16591_FER_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q29FA1_Q29FA1_DROPS_46245 and tr_B4H1L5_B4H1L5_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2Q9E1_H2Q9E1_PANTR_9598 and tr_A0A2R9CBX3_A0A2R9CBX3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R8L2_H2R8L2_PANTR_9598 and tr_A0A2R9ADH9_A0A2R9ADH9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7A7H5_F7A7H5_MACMU_9544 and tr_G7PBA3_G7PBA3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7A7H5_F7A7H5_MACMU_9544 and tr_A0A2K6CJ02_A0A2K6CJ02_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GUD3_F7GUD3_MACMU_9544 and tr_A0A0D9RRH1_A0A0D9RRH1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GUD3_F7GUD3_MACMU_9544 and tr_A0A2K5NKC8_A0A2K5NKC8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GUD3_F7GUD3_MACMU_9544 and tr_A0A2K5YE13_A0A2K5YE13_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7H023_F7H023_MACMU_9544 and tr_G7NTP3_G7NTP3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HPR8_F7HPR8_MACMU_9544 and tr_G7NUJ6_G7NUJ6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HPR8_F7HPR8_MACMU_9544 and tr_A0A2K6DER0_A0A2K6DER0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HPR8_F7HPR8_MACMU_9544 and tr_A0A2K6A6Y1_A0A2K6A6Y1_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0Z659_H0Z659_TAEGU_59729 and tr_A0A218VEW8_A0A218VEW8_9PASE_299123 are exactly identical! WARNING: Sequences tr_G1MAQ2_G1MAQ2_AILME_9646 and tr_A0A337RXI4_A0A337RXI4_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A140T848_A0A140T848_BOVIN_9913 and sp_Q58DL5_BCAR3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A091IRN3_A0A091IRN3_EGRGA_188379 and tr_A0A0A0A4N8_A0A0A0A4N8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CW81_A0A0V1CW81_TRIBR_45882 and tr_A0A0V0XA45_A0A0V0XA45_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CW81_A0A0V1CW81_TRIBR_45882 and tr_A0A0V0V2B3_A0A0V0V2B3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CW81_A0A0V1CW81_TRIBR_45882 and tr_A0A0V1LLY7_A0A0V1LLY7_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CW81_A0A0V1CW81_TRIBR_45882 and tr_A0A0V0ZUL5_A0A0V0ZUL5_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CW81_A0A0V1CW81_TRIBR_45882 and tr_A0A0V0U2G9_A0A0V0U2G9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0UXM8_A0A0V0UXM8_9BILA_181606 and tr_A0A0V1L531_A0A0V1L531_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1KZ99_A0A0V1KZ99_9BILA_6335 and tr_A0A0V0ZI64_A0A0V0ZI64_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1KZ99_A0A0V1KZ99_9BILA_6335 and tr_A0A0V1P7Q6_A0A0V1P7Q6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1KZ99_A0A0V1KZ99_9BILA_6335 and tr_A0A0V0UAN6_A0A0V0UAN6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A2D0Q463_A0A2D0Q463_ICTPU_7998 and tr_A0A2D0Q6W4_A0A2D0Q6W4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5MFT1_A0A2K5MFT1_CERAT_9531 and tr_A0A2K5Z8U0_A0A2K5Z8U0_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 34 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P98077/4_raxmlng_ancestral/P98077.raxml.reduced.phy Alignment comprises 1 partitions and 582 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 582 Gaps: 43.04 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P98077/4_raxmlng_ancestral/P98077.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_300621/phylogeny-snakemake/results/P98077/3_mltree/P98077.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 146 / 11680 [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: -206933.560781 [00:00:00 -206933.560781] Initial branch length optimization [00:00:01 -175367.670662] Model parameter optimization (eps = 0.100000) [00:01:07] Tree #1, final logLikelihood: -174622.889668 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.128086,2.223635) (0.053562,0.132437) (0.331072,0.470132) (0.487280,1.133728) 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_300621/phylogeny-snakemake/results/P98077/4_raxmlng_ancestral/P98077.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P98077/4_raxmlng_ancestral/P98077.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P98077/4_raxmlng_ancestral/P98077.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P98077/4_raxmlng_ancestral/P98077.raxml.log Analysis started: 20-Jul-2021 16:35:11 / finished: 20-Jul-2021 16:36:24 Elapsed time: 73.047 seconds