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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 03-Jun-2021 02:37:21 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/2_msa/Q93099_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/3_mltree/Q93099.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/4_raxmlng_ancestral/Q93099 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677041 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/2_msa/Q93099_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 445 sites WARNING: Sequences tr_B6Q563_B6Q563_TALMQ_441960 and tr_A0A093VJR0_A0A093VJR0_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B6Q786_B6Q786_TALMQ_441960 and tr_A0A093VNA7_A0A093VNA7_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2VTN5_B2VTN5_PYRTR_426418 and tr_A0A2W1EPZ7_A0A2W1EPZ7_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B2WCH2_B2WCH2_PYRTR_426418 and tr_A0A2W1E8W9_A0A2W1E8W9_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B2WNC9_B2WNC9_PYRTR_426418 and tr_A0A2W1GR90_A0A2W1GR90_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8N2C4_B8N2C4_ASPFN_332952 and tr_Q2ULZ3_Q2ULZ3_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N2C4_B8N2C4_ASPFN_332952 and tr_A0A0F0IA50_A0A0F0IA50_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8N2C4_B8N2C4_ASPFN_332952 and tr_A0A1S9DNT3_A0A1S9DNT3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8N2C4_B8N2C4_ASPFN_332952 and tr_A0A2G7G9J4_A0A2G7G9J4_9EURO_656916 are exactly identical! WARNING: Sequences tr_B8N5U4_B8N5U4_ASPFN_332952 and tr_A0A1S9DPE7_A0A1S9DPE7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UK12_A0A179UK12_BLAGS_559298 and tr_C5GTL4_C5GTL4_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QN64_H2QN64_PANTR_9598 and tr_A0A2R9AGX4_A0A2R9AGX4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9GDV2_F9GDV2_FUSOF_660025 and tr_S0E3E7_S0E3E7_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9GDV2_F9GDV2_FUSOF_660025 and tr_N4V049_N4V049_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9GDV2_F9GDV2_FUSOF_660025 and tr_A0A2H3T5H6_A0A2H3T5H6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_C6HD19_C6HD19_AJECH_544712 and tr_F0UTU0_F0UTU0_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0HJK1_A0A0E0HJK1_ORYNI_4536 and tr_B8B197_B8B197_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HJK1_A0A0E0HJK1_ORYNI_4536 and tr_I1PYQ2_I1PYQ2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HJK1_A0A0E0HJK1_ORYNI_4536 and tr_A0A0E0PSC7_A0A0E0PSC7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HJK1_A0A0E0HJK1_ORYNI_4536 and tr_A0A0D3GBS5_A0A0D3GBS5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0HJK1_A0A0E0HJK1_ORYNI_4536 and tr_A0A0E0A3T8_A0A0E0A3T8_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0HJK1_A0A0E0HJK1_ORYNI_4536 and sp_Q5VRH4_HGD_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QVP6_A2QVP6_ASPNC_425011 and tr_G3YCA2_G3YCA2_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QVP6_A2QVP6_ASPNC_425011 and tr_A0A319AMZ6_A0A319AMZ6_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XAT0_G7XAT0_ASPKW_1033177 and tr_A0A146F857_A0A146F857_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XAT0_G7XAT0_ASPKW_1033177 and tr_A0A317US72_A0A317US72_9EURO_1448314 are exactly identical! WARNING: Sequences tr_G7XB63_G7XB63_ASPKW_1033177 and tr_A0A317ULN6_A0A317ULN6_9EURO_1448314 are exactly identical! WARNING: Sequences tr_F4PCZ0_F4PCZ0_BATDJ_684364 and tr_A0A177WYN8_A0A177WYN8_BATDE_403673 are exactly identical! WARNING: Sequences tr_G2Y4I0_G2Y4I0_BOTF4_999810 and tr_M7U880_M7U880_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SDN5_F2SDN5_TRIRC_559305 and tr_A0A059J5V8_A0A059J5V8_9EURO_1215338 are exactly identical! WARNING: Sequences tr_F2SDN5_F2SDN5_TRIRC_559305 and tr_A0A178EV33_A0A178EV33_TRIRU_5551 are exactly identical! WARNING: Sequences tr_N4TPB8_N4TPB8_FUSC1_1229664 and tr_X0D5J3_X0D5J3_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_N4TPB8_N4TPB8_FUSC1_1229664 and tr_A0A2H3TUR7_A0A2H3TUR7_FUSOX_5507 are exactly identical! WARNING: Sequences tr_V2XTP7_V2XTP7_MONRO_1381753 and tr_A0A0W0EXK0_A0A0W0EXK0_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2RJM4_W2RJM4_PHYPN_761204 and tr_W2JUP7_W2JUP7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015KSS9_A0A015KSS9_9GLOM_1432141 and tr_U9TXW6_U9TXW6_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067ETR6_A0A067ETR6_CITSI_2711 and tr_A0A2H5PU20_A0A2H5PU20_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A094ENW8_A0A094ENW8_9PEZI_1420912 and tr_A0A1B8GNA0_A0A1B8GNA0_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094GD93_A0A094GD93_9PEZI_1420912 and tr_A0A1B8G6L9_A0A1B8G6L9_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0A1NER1_A0A0A1NER1_9FUNG_58291 and tr_A0A2G4SJX9_A0A2G4SJX9_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0A1NER1_A0A0A1NER1_9FUNG_58291 and tr_A0A367JT01_A0A367JT01_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1NUU1_A0A0A1NUU1_9FUNG_58291 and tr_A0A367KGP0_A0A367KGP0_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A2K6CGJ6_A0A2K6CGJ6_MACNE_9545 and tr_A0A2K5XMU7_A0A2K5XMU7_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 43 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/4_raxmlng_ancestral/Q93099.raxml.reduced.phy Alignment comprises 1 partitions and 445 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 445 Gaps: 4.19 % Invariant sites: 2.92 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/4_raxmlng_ancestral/Q93099.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/3_mltree/Q93099.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 112 / 8960 [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: -172689.333462 [00:00:00 -172689.333462] Initial branch length optimization [00:00:01 -172386.367912] Model parameter optimization (eps = 0.100000) [00:00:24] Tree #1, final logLikelihood: -171665.197534 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.257023,0.374414) (0.324474,0.524949) (0.238755,1.074762) (0.179747,2.652780) 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/4_raxmlng_ancestral/Q93099.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/4_raxmlng_ancestral/Q93099.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/4_raxmlng_ancestral/Q93099.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q93099/4_raxmlng_ancestral/Q93099.raxml.log Analysis started: 03-Jun-2021 02:37:21 / finished: 03-Jun-2021 02:37:49 Elapsed time: 28.077 seconds Consumed energy: 2.195 Wh