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 14-Jul-2021 15:05:14 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/2_msa/P52848_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/3_mltree/P52848.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/4_raxmlng_ancestral/P52848 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626264314 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/P52848/2_msa/P52848_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 882 sites WARNING: Sequences sp_Q673U1_HS3S2_MOUSE_10090 and sp_Q80W66_HS3S2_RAT_10116 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2J8U159_A0A2J8U159_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_F7IAJ7_F7IAJ7_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_G7P3M0_G7P3M0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A096MX52_A0A096MX52_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2K5L8U9_A0A2K5L8U9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2K6BWI1_A0A2K6BWI1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2K5XKT5_A0A2K5XKT5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2R8ZRJ5_A0A2R8ZRJ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_H2QAR3_H2QAR3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and sp_Q9Y278_HS3S2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A096NHD6_A0A096NHD6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A0D9R3M4_A0A0D9R3M4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A2K5N5Q6_A0A2K5N5Q6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A2K6CDE8_A0A2K6CDE8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A2R9B8Q8_A0A2R9B8Q8_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R584_H2R584_PANTR_9598 and tr_A0A2R9AYT7_A0A2R9AYT7_PANPA_9597 are exactly identical! WARNING: Sequences tr_M4A4T6_M4A4T6_XIPMA_8083 and tr_A0A087Y103_A0A087Y103_POEFO_48698 are exactly identical! WARNING: Sequences tr_F7DZJ3_F7DZJ3_MACMU_9544 and tr_A0A096MX80_A0A096MX80_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DZJ3_F7DZJ3_MACMU_9544 and tr_A0A2K5NHZ7_A0A2K5NHZ7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DZJ3_F7DZJ3_MACMU_9544 and tr_A0A2K5YXZ7_A0A2K5YXZ7_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GSZ9_F7GSZ9_MACMU_9544 and tr_G7P8P9_G7P8P9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GSZ9_F7GSZ9_MACMU_9544 and tr_A0A2K5LGQ2_A0A2K5LGQ2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GSZ9_F7GSZ9_MACMU_9544 and tr_A0A2K6CHB2_A0A2K6CHB2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HFM8_F7HFM8_MACMU_9544 and tr_G7P653_G7P653_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HFM8_F7HFM8_MACMU_9544 and tr_A0A2K6CK99_A0A2K6CK99_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZFK1_H0ZFK1_TAEGU_59729 and tr_A0A091EAX4_A0A091EAX4_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZFK1_H0ZFK1_TAEGU_59729 and tr_A0A093PIZ9_A0A093PIZ9_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZNZ3_H0ZNZ3_TAEGU_59729 and tr_A0A218UX55_A0A218UX55_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A044TS16_A0A044TS16_ONCVO_6282 and tr_A0A182E006_A0A182E006_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096MY37_A0A096MY37_PAPAN_9555 and tr_A0A2K5L8W4_A0A2K5L8W4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P2Z1_A0A096P2Z1_PAPAN_9555 and tr_A0A0D9R9H6_A0A0D9R9H6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P2Z1_A0A096P2Z1_PAPAN_9555 and tr_A0A2K5P3K2_A0A2K5P3K2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P4L1_A0A096P4L1_PAPAN_9555 and tr_A0A2K6BWF2_A0A2K6BWF2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091UKI3_A0A091UKI3_NIPNI_128390 and tr_A0A0A0ANY3_A0A0A0ANY3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087QYU7_A0A087QYU7_APTFO_9233 and tr_A0A1V4KJD4_A0A1V4KJD4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A151X1F8_A0A151X1F8_9HYME_64791 and tr_A0A195EUE6_A0A195EUE6_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A226MVT5_A0A226MVT5_CALSU_9009 and tr_A0A226P8F4_A0A226P8F4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5LUT4_A0A2K5LUT4_CERAT_9531 and tr_A0A2K5YYW3_A0A2K5YYW3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5MRU1_A0A2K5MRU1_CERAT_9531 and tr_A0A2K5Z088_A0A2K5Z088_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4A8M0_A0A2U4A8M0_TURTR_9739 and tr_A0A2Y9PB65_A0A2Y9PB65_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A8M6_A0A2U4A8M6_TURTR_9739 and tr_A0A2Y9PEE9_A0A2Y9PEE9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3W465_A0A2U3W465_ODORO_9708 and tr_A0A2U3YC72_A0A2U3YC72_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 43 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/P52848/4_raxmlng_ancestral/P52848.raxml.reduced.phy Alignment comprises 1 partitions and 882 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 882 Gaps: 36.26 % Invariant sites: 0.11 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/4_raxmlng_ancestral/P52848.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/P52848/3_mltree/P52848.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 221 / 17680 [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: -191993.420416 [00:00:00 -191993.420416] Initial branch length optimization [00:00:01 -187551.110409] Model parameter optimization (eps = 0.100000) [00:00:52] Tree #1, final logLikelihood: -187120.040616 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.146103,0.326571) (0.203566,0.385881) (0.370599,0.907563) (0.279732,1.921101) 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/P52848/4_raxmlng_ancestral/P52848.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/4_raxmlng_ancestral/P52848.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/4_raxmlng_ancestral/P52848.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/4_raxmlng_ancestral/P52848.raxml.log Analysis started: 14-Jul-2021 15:05:14 / finished: 14-Jul-2021 15:06:13 Elapsed time: 59.817 seconds