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 17-Jul-2021 09:02:14 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NDG6/2_msa/Q8NDG6_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NDG6/3_mltree/Q8NDG6.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NDG6/4_raxmlng_ancestral/Q8NDG6 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626501734 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/Q8NDG6/2_msa/Q8NDG6_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1382 sites WARNING: Sequences tr_M3YJE6_M3YJE6_MUSPF_9669 and tr_G1L659_G1L659_AILME_9646 are exactly identical! WARNING: Sequences tr_G1S8P5_G1S8P5_NOMLE_61853 and tr_G3SFU0_G3SFU0_GORGO_9595 are exactly identical! WARNING: Sequences tr_B6Q8Y8_B6Q8Y8_TALMQ_441960 and tr_A0A093VBW1_A0A093VBW1_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WNJ0_B2WNJ0_PYRTR_426418 and tr_A0A2W1E7Q6_A0A2W1E7Q6_9PLEO_45151 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and tr_H2Q0R0_H2Q0R0_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and sp_Q08211_DHX9_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and tr_F6W5Y4_F6W5Y4_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and tr_G7NXG8_G7NXG8_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and tr_A0A2K6DJY7_A0A2K6DJY7_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and tr_A0A2R9AB38_A0A2R9AB38_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q7Z478_DHX29_HUMAN_9606 and tr_A0A2R9C7X8_A0A2R9C7X8_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q9H2U1_DHX36_HUMAN_9606 and tr_A0A2R8ZLR2_A0A2R8ZLR2_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7D9X5_F7D9X5_MACMU_9544 and tr_A0A2K5MNR8_A0A2K5MNR8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7D9X5_F7D9X5_MACMU_9544 and tr_A0A2K6B4G5_A0A2K6B4G5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H061_F7H061_MACMU_9544 and tr_G7PM23_G7PM23_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H061_F7H061_MACMU_9544 and tr_A0A096N5W6_A0A096N5W6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H061_F7H061_MACMU_9544 and tr_A0A2K6DC36_A0A2K6DC36_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H061_F7H061_MACMU_9544 and tr_A0A2K5Y680_A0A2K5Y680_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7NZL0_G7NZL0_MACFA_9541 and tr_A0A096N6F2_A0A096N6F2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NZL0_G7NZL0_MACFA_9541 and tr_A0A2K5MTE8_A0A2K5MTE8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NZL0_G7NZL0_MACFA_9541 and tr_A0A2K6DAR7_A0A2K6DAR7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NZL0_G7NZL0_MACFA_9541 and tr_A0A2K5YP21_A0A2K5YP21_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5E5N3_G5E5N3_BOVIN_9913 and sp_Q28141_DHX9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_L0PAW8_L0PAW8_PNEJ8_1209962 and tr_A0A0W4ZJR4_A0A0W4ZJR4_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_A0A015J9A9_A0A015J9A9_9GLOM_1432141 and tr_U9SXS5_U9SXS5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096NWR7_A0A096NWR7_PAPAN_9555 and tr_A0A2K5L8V6_A0A2K5L8V6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NWR7_A0A096NWR7_PAPAN_9555 and tr_A0A2K5ZUW5_A0A2K5ZUW5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A078J242_A0A078J242_BRANA_3708 and tr_A0A0D3D9Z7_A0A0D3D9Z7_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094GLD0_A0A094GLD0_9PEZI_1420912 and tr_A0A1B8GMZ7_A0A1B8GMZ7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0A1ML61_A0A0A1ML61_9FUNG_58291 and tr_A0A367KCK6_A0A367KCK6_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091IXG9_A0A091IXG9_EGRGA_188379 and tr_A0A091W2D4_A0A091W2D4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1S3ZIW7_A0A1S3ZIW7_TOBAC_4097 and tr_A0A1U7WAQ9_A0A1U7WAQ9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A3Q0FCC0_A0A3Q0FCC0_VIGRR_3916 and tr_A0A3Q0FFZ8_A0A3Q0FFZ8_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A1U8G467_A0A1U8G467_CAPAN_4072 and tr_A0A2G3CZW0_A0A2G3CZW0_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2U3VP84_A0A2U3VP84_ODORO_9708 and tr_A0A2U3XD06_A0A2U3XD06_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3VP84_A0A2U3VP84_ODORO_9708 and tr_A0A2Y9JTC9_A0A2Y9JTC9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2U3VP84_A0A2U3VP84_ODORO_9708 and tr_A0A384CX23_A0A384CX23_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 37 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/Q8NDG6/4_raxmlng_ancestral/Q8NDG6.raxml.reduced.phy Alignment comprises 1 partitions and 1382 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1382 Gaps: 39.73 % Invariant sites: 0.87 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NDG6/4_raxmlng_ancestral/Q8NDG6.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/Q8NDG6/3_mltree/Q8NDG6.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 346 / 27680 [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: -452249.698232 [00:00:00 -452249.698232] Initial branch length optimization [00:00:02 -450884.990305] Model parameter optimization (eps = 0.100000) [00:01:06] Tree #1, final logLikelihood: -449923.277460 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.124710,0.235682) (0.201551,0.309214) (0.337569,0.854252) (0.336170,1.844055) 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/Q8NDG6/4_raxmlng_ancestral/Q8NDG6.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NDG6/4_raxmlng_ancestral/Q8NDG6.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NDG6/4_raxmlng_ancestral/Q8NDG6.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NDG6/4_raxmlng_ancestral/Q8NDG6.raxml.log Analysis started: 17-Jul-2021 09:02:14 / finished: 17-Jul-2021 09:03:32 Elapsed time: 78.151 seconds