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 13:47:59 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BWV7/2_msa/Q9BWV7_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BWV7/3_mltree/Q9BWV7.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BWV7/4_raxmlng_ancestral/Q9BWV7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803679 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/Q9BWV7/2_msa/Q9BWV7_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 592 sites WARNING: Sequences tr_B4QUB7_B4QUB7_DROSI_7240 and tr_B4IJG3_B4IJG3_DROSE_7238 are exactly identical! WARNING: Sequences tr_F1NZA9_F1NZA9_CHICK_9031 and tr_G1NLX9_G1NLX9_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NZA9_F1NZA9_CHICK_9031 and tr_A0A091V0Y3_A0A091V0Y3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_F1NZA9_F1NZA9_CHICK_9031 and tr_A0A091VWF5_A0A091VWF5_OPIHO_30419 are exactly identical! WARNING: Sequences tr_F1NZA9_F1NZA9_CHICK_9031 and tr_A0A0A0A4N5_A0A0A0A4N5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_F1NZA9_F1NZA9_CHICK_9031 and tr_A0A1V4K4Z2_A0A1V4K4Z2_PATFA_372326 are exactly identical! WARNING: Sequences tr_M3YXY6_M3YXY6_MUSPF_9669 and tr_A0A2U3ZCW0_A0A2U3ZCW0_ODORO_9708 are exactly identical! WARNING: Sequences tr_G3RKN6_G3RKN6_GORGO_9595 and tr_H2NLU9_H2NLU9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RKN6_G3RKN6_GORGO_9595 and sp_Q6EMB2_TTLL5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RKN6_G3RKN6_GORGO_9595 and tr_A0A2R9C5J7_A0A2R9C5J7_PANPA_9597 are exactly identical! WARNING: Sequences tr_C3ZM76_C3ZM76_BRAFL_7739 and tr_C3ZM80_C3ZM80_BRAFL_7739 are exactly identical! WARNING: Sequences tr_H2P4N4_H2P4N4_PONAB_9601 and sp_O95922_TTLL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2P4N4_H2P4N4_PONAB_9601 and tr_A0A2R9C6E1_A0A2R9C6E1_PANPA_9597 are exactly identical! WARNING: Sequences tr_E2RTA4_E2RTA4_CANLF_9615 and tr_A0A096NKG4_A0A096NKG4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_E2RTA4_E2RTA4_CANLF_9615 and tr_A0A0D9QZZ2_A0A0D9QZZ2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2R872_H2R872_PANTR_9598 and tr_A0A2R8ZPT8_A0A2R8ZPT8_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6QDV6_F6QDV6_HORSE_9796 and sp_Q5PPI9_TTLL1_RAT_10116 are exactly identical! WARNING: Sequences tr_F6QDV6_F6QDV6_HORSE_9796 and sp_Q0VC71_TTLL1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q14679_TTLL4_HUMAN_9606 and tr_A0A2R8ZTV6_A0A2R8ZTV6_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7HD26_F7HD26_MACMU_9544 and tr_G7P2C8_G7P2C8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HD26_F7HD26_MACMU_9544 and tr_A0A0D9R8H6_A0A0D9R8H6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HD26_F7HD26_MACMU_9544 and tr_A0A2K6DDB4_A0A2K6DDB4_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZP67_H0ZP67_TAEGU_59729 and tr_A0A218UKQ1_A0A218UKQ1_9PASE_299123 are exactly identical! WARNING: Sequences tr_W2PG00_W2PG00_PHYPN_761204 and tr_A0A0W8CKV9_A0A0W8CKV9_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A091VC39_A0A091VC39_NIPNI_128390 and tr_A0A0A0AF04_A0A0A0AF04_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1S3N0I0_A0A1S3N0I0_SALSA_8030 and tr_A0A1S3SI06_A0A1S3SI06_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1Y2B6Y8_A0A1Y2B6Y8_9FUNG_329046 and tr_A0A1Y2CLJ0_A0A1Y2CLJ0_9FUNG_329046 are exactly identical! WARNING: Sequences tr_A0A226NI11_A0A226NI11_CALSU_9009 and tr_A0A226NZX2_A0A226NZX2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RN91_A0A2D0RN91_ICTPU_7998 and tr_A0A2D0RN95_A0A2D0RN95_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RN91_A0A2D0RN91_ICTPU_7998 and tr_A0A2D0RN98_A0A2D0RN98_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9JSV8_A0A2Y9JSV8_ENHLU_391180 and tr_A0A384CS76_A0A384CS76_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 31 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/Q9BWV7/4_raxmlng_ancestral/Q9BWV7.raxml.reduced.phy Alignment comprises 1 partitions and 592 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 592 Gaps: 34.58 % Invariant sites: 0.17 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BWV7/4_raxmlng_ancestral/Q9BWV7.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/Q9BWV7/3_mltree/Q9BWV7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 148 / 11840 [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: -227047.129382 [00:00:00 -227047.129382] Initial branch length optimization [00:00:01 -218423.477309] Model parameter optimization (eps = 0.100000) [00:00:37] Tree #1, final logLikelihood: -217934.928577 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.096907,0.219416) (0.161974,0.290191) (0.265654,0.692961) (0.475466,1.572450) 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/Q9BWV7/4_raxmlng_ancestral/Q9BWV7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BWV7/4_raxmlng_ancestral/Q9BWV7.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BWV7/4_raxmlng_ancestral/Q9BWV7.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BWV7/4_raxmlng_ancestral/Q9BWV7.raxml.log Analysis started: 04-Jun-2021 13:47:59 / finished: 04-Jun-2021 13:48:42 Elapsed time: 42.785 seconds