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 14:57:13 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37287/2_msa/P37287_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37287/3_mltree/P37287.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37287/4_raxmlng_ancestral/P37287 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635033 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/P37287/2_msa/P37287_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 484 sites WARNING: Sequences tr_A0A0E1RWH7_A0A0E1RWH7_COCIM_246410 and tr_E9DH81_E9DH81_COCPS_443226 are exactly identical! WARNING: Sequences tr_B2WKH8_B2WKH8_PYRTR_426418 and tr_A0A2W1EEX7_A0A2W1EEX7_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A179UYQ2_A0A179UYQ2_BLAGS_559298 and tr_C5GLR9_C5GLR9_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QYB7_H2QYB7_PANTR_9598 and tr_A0A2R9C7Y2_A0A2R9C7Y2_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FTX2_F9FTX2_FUSOF_660025 and tr_N4TQF6_N4TQF6_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FTX2_F9FTX2_FUSOF_660025 and tr_X0CPI6_X0CPI6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FTX2_F9FTX2_FUSOF_660025 and tr_A0A2H3SRX9_A0A2H3SRX9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FTX2_F9FTX2_FUSOF_660025 and tr_A0A2H3HWN2_A0A2H3HWN2_FUSOX_327505 are exactly identical! WARNING: Sequences tr_E9ENQ1_E9ENQ1_METRA_655844 and tr_A0A0B4IGX4_A0A0B4IGX4_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9ENQ1_E9ENQ1_METRA_655844 and tr_A0A0D9P5R8_A0A0D9P5R8_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6HN71_C6HN71_AJECH_544712 and tr_F0UF42_F0UF42_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A158NHG6_A0A158NHG6_ATTCE_12957 and tr_A0A195AV25_A0A195AV25_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0H5S972_A0A0H5S972_BRUMA_6279 and tr_A0A0R3QM14_A0A0R3QM14_9BILA_42155 are exactly identical! WARNING: Sequences tr_B8B502_B8B502_ORYSI_39946 and tr_B7F9D1_B7F9D1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1Q9N5_I1Q9N5_ORYGL_4538 and tr_A0A0D3GPG5_A0A0D3GPG5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1Q9N5_I1Q9N5_ORYGL_4538 and tr_A0A0E0AHY9_A0A0E0AHY9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F9X3W1_F9X3W1_ZYMTI_336722 and tr_A0A1X7RKH3_A0A1X7RKH3_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XSB3_G2XSB3_BOTF4_999810 and tr_M7UIF9_M7UIF9_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_G7Q296_G7Q296_MACFA_9541 and tr_A0A2K6E338_A0A2K6E338_MACNE_9545 are exactly identical! WARNING: Sequences tr_U5H4E0_U5H4E0_USTV1_683840 and tr_A0A2X0M8A1_A0A2X0M8A1_9BASI_796604 are exactly identical! WARNING: Sequences tr_W2PBB3_W2PBB3_PHYPN_761204 and tr_A0A0W8CX15_A0A0W8CX15_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PBB3_W2PBB3_PHYPN_761204 and tr_W2LC05_W2LC05_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A096MPA0_A0A096MPA0_PAPAN_9555 and tr_A0A0D9RR40_A0A0D9RR40_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MPA0_A0A096MPA0_PAPAN_9555 and tr_A0A2K5NBD0_A0A2K5NBD0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A094CWU4_A0A094CWU4_9PEZI_1420910 and tr_A0A1B8DSX4_A0A1B8DSX4_9PEZI_1524831 are exactly identical! WARNING: Sequences tr_A0A094ENW9_A0A094ENW9_9PEZI_1420912 and tr_A0A1B8GHP9_A0A1B8GHP9_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0D2RMK4_A0A0D2RMK4_GOSRA_29730 and tr_A0A1U8LG94_A0A1U8LG94_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0F9X080_A0A0F9X080_TRIHA_5544 and tr_A0A2T4A014_A0A2T4A014_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0L7K3A9_A0A0L7K3A9_9NEOP_104452 and tr_A0A0L7KLE8_A0A0L7KLE8_9NEOP_104452 are exactly identical! WARNING: Sequences tr_A0A0G4PKA2_A0A0G4PKA2_PENCA_1429867 and tr_A0A1V6QWM4_A0A1V6QWM4_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A117DV38_A0A117DV38_ASPNG_5061 and tr_A0A1L9NBB4_A0A1L9NBB4_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A117DV38_A0A117DV38_ASPNG_5061 and tr_A0A317VTM9_A0A317VTM9_9EURO_1448314 are exactly identical! WARNING: Sequences tr_I1RBN0_I1RBN0_GIBZE_229533 and tr_A0A2T4HA19_A0A2T4HA19_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A164YR89_A0A164YR89_9HOMO_1314777 and tr_A0A166GE74_A0A166GE74_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S3XZZ1_A0A1S3XZZ1_TOBAC_4097 and tr_A0A1U7WB79_A0A1U7WB79_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1B8C5F7_A0A1B8C5F7_9PEZI_1622147 and tr_A0A1B8EV76_A0A1B8EV76_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A1R3RL64_A0A1R3RL64_ASPC5_602072 and tr_A0A317XAS2_A0A317XAS2_9EURO_1450535 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_020621/phylogeny-snakemake/results/P37287/4_raxmlng_ancestral/P37287.raxml.reduced.phy Alignment comprises 1 partitions and 484 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 484 Gaps: 14.48 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37287/4_raxmlng_ancestral/P37287.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/P37287/3_mltree/P37287.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 121 / 9680 [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: -194007.018501 [00:00:00 -194007.018501] Initial branch length optimization [00:00:01 -193621.660693] Model parameter optimization (eps = 0.100000) [00:00:40] Tree #1, final logLikelihood: -192652.777437 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.214350,0.288400) (0.250281,0.346075) (0.281945,0.793501) (0.253425,2.477427) 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/P37287/4_raxmlng_ancestral/P37287.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37287/4_raxmlng_ancestral/P37287.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37287/4_raxmlng_ancestral/P37287.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P37287/4_raxmlng_ancestral/P37287.raxml.log Analysis started: 02-Jun-2021 14:57:13 / finished: 02-Jun-2021 14:58:00 Elapsed time: 47.102 seconds