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 02-Jun-2021 14:54:22 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q14203/2_msa/Q14203_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q14203/3_mltree/Q14203.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q14203/4_raxmlng_ancestral/Q14203 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622634862 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/Q14203/2_msa/Q14203_nogap_msa.fasta [00:00:00] Loaded alignment with 968 taxa and 1278 sites WARNING: Sequences tr_M3Y2Q6_M3Y2Q6_MUSPF_9669 and tr_A0A2Y9L524_A0A2Y9L524_ENHLU_391180 are exactly identical! WARNING: Sequences tr_B8PE70_B8PE70_POSPM_561896 and tr_A0A1X6NFD6_A0A1X6NFD6_9APHY_670580 are exactly identical! WARNING: Sequences tr_Q2M015_Q2M015_DROPS_46245 and tr_B4H8Z3_B4H8Z3_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2QG58_H2QG58_PANTR_9598 and sp_Q99426_TBCB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QG58_H2QG58_PANTR_9598 and tr_A0A2R9CG94_A0A2R9CG94_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R8W0_H2R8W0_PANTR_9598 and tr_A0A2R9C5J0_A0A2R9C5J0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6UNW8_F6UNW8_HORSE_9796 and tr_G1L2E7_G1L2E7_AILME_9646 are exactly identical! WARNING: Sequences tr_F6T5J5_F6T5J5_MACMU_9544 and tr_A0A096NGM6_A0A096NGM6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6T5J5_F6T5J5_MACMU_9544 and tr_A0A2K5KZX9_A0A2K5KZX9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6T5J5_F6T5J5_MACMU_9544 and tr_A0A2K6E3S4_A0A2K6E3S4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6T5J5_F6T5J5_MACMU_9544 and tr_A0A2K5ZGC1_A0A2K5ZGC1_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9EMA0_H9EMA0_MACMU_9544 and tr_A0A2I3M6K5_A0A2I3M6K5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9EMA0_H9EMA0_MACMU_9544 and tr_A0A0D9QW67_A0A0D9QW67_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H9EMA0_H9EMA0_MACMU_9544 and tr_A0A2K5KJB3_A0A2K5KJB3_CERAT_9531 are exactly identical! WARNING: Sequences tr_H9EMA0_H9EMA0_MACMU_9544 and tr_A0A2K6D9B4_A0A2K6D9B4_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9EMA0_H9EMA0_MACMU_9544 and tr_A0A2K5YXA4_A0A2K5YXA4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PLY6_G7PLY6_MACFA_9541 and tr_A0A0D9REF7_A0A0D9REF7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PLY6_G7PLY6_MACFA_9541 and tr_A0A2K5P3N6_A0A2K5P3N6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PLY6_G7PLY6_MACFA_9541 and tr_A0A2K6AM52_A0A2K6AM52_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PLY6_G7PLY6_MACFA_9541 and tr_A0A2K6AB73_A0A2K6AB73_MANLE_9568 are exactly identical! WARNING: Sequences tr_U3IS85_U3IS85_ANAPL_8839 and tr_A0A091F110_A0A091F110_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3IS85_U3IS85_ANAPL_8839 and tr_A0A091IRG2_A0A091IRG2_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3IS85_U3IS85_ANAPL_8839 and tr_A0A087RI16_A0A087RI16_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3IS85_U3IS85_ANAPL_8839 and tr_A0A099YX53_A0A099YX53_TINGU_94827 are exactly identical! WARNING: Sequences tr_U3IS85_U3IS85_ANAPL_8839 and tr_A0A091FV25_A0A091FV25_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3IS85_U3IS85_ANAPL_8839 and tr_A0A093G376_A0A093G376_DRYPU_118200 are exactly identical! WARNING: Sequences tr_V2X8S4_V2X8S4_MONRO_1381753 and tr_A0A0W0FS59_A0A0W0FS59_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PLY4_W2PLY4_PHYPN_761204 and tr_A0A0W8CDC5_A0A0W8CDC5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PLY4_W2PLY4_PHYPN_761204 and tr_W2FYV5_W2FYV5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QFN0_W2QFN0_PHYPN_761204 and tr_W2LJD6_W2LJD6_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015IR27_A0A015IR27_9GLOM_1432141 and tr_A0A2I1GI81_A0A2I1GI81_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A044UHD1_A0A044UHD1_ONCVO_6282 and tr_A0A182EP32_A0A182EP32_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0A1N0A4_A0A0A1N0A4_9FUNG_58291 and tr_A0A0A1NRS8_A0A0A1NRS8_9FUNG_58291 are exactly identical! WARNING: Sequences tr_A0A0A1N0A4_A0A0A1N0A4_9FUNG_58291 and tr_A0A367J755_A0A367J755_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091IP81_A0A091IP81_EGRGA_188379 and tr_A0A087RI17_A0A087RI17_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IP81_A0A091IP81_EGRGA_188379 and tr_A0A0A0AIR7_A0A0A0AIR7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1D1VRQ2_A0A1D1VRQ2_RAMVA_947166 and tr_A0A1D1VYZ7_A0A1D1VYZ7_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A1R1XAH0_A0A1R1XAH0_9FUNG_133412 and tr_A0A1R1XZR7_A0A1R1XZR7_9FUNG_133412 are exactly identical! WARNING: Sequences tr_A0A2Y9PFY5_A0A2Y9PFY5_DELLE_9749 and tr_A0A383YR89_A0A383YR89_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 39 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/Q14203/4_raxmlng_ancestral/Q14203.raxml.reduced.phy Alignment comprises 1 partitions and 1278 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1278 Gaps: 52.15 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q14203/4_raxmlng_ancestral/Q14203.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/Q14203/3_mltree/Q14203.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 320 / 25600 [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: -912018.054824 [00:00:00 -912018.054824] Initial branch length optimization [00:00:06 -582677.291919] Model parameter optimization (eps = 0.100000) [00:02:09] Tree #1, final logLikelihood: -579972.427672 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.102906,0.714617) (0.065002,0.820651) (0.378137,0.721432) (0.453956,1.322416) 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/Q14203/4_raxmlng_ancestral/Q14203.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q14203/4_raxmlng_ancestral/Q14203.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q14203/4_raxmlng_ancestral/Q14203.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q14203/4_raxmlng_ancestral/Q14203.raxml.log Analysis started: 02-Jun-2021 14:54:22 / finished: 02-Jun-2021 14:56:42 Elapsed time: 140.301 seconds